BMRB Entry 34308

Name: Active-site conformational dynamics of carbonic anhydrase II under native conditions: An NMR perspective
Published: 2019-08-23

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PDB ID: 6hd2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34308
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Active-site conformational dynamics of carbonic anhydrase II under native conditions: An NMR perspective

Deposition date:

2018-08-17

Original release date:

2019-08-23

Authors:

Singh, H.; Linser, R.

Citation:

Citation: Singh, Himanshu; Vasa, Suresh; Jangra, Harish; Rovo, Petra; Paslack, Christopher; Das, Chandan; Zipse, Hendrik; Schafer, Lars; Linser, Rasmus. "Fast Microsecond Dynamics of the Protein-Water Network in the Active Site of Human Carbonic Anhydrase II Studied by Solid-State NMR Spectroscopy" J. Am. Chem. Soc. 141, 19276-19288 (2019).
PubMed: 31647225

Assembly members:

Assembly members:
entity_1, polymer, 260 residues, 29289.062 Da.
entity_ZN, non-polymer, 65.409 Da.
entity_HOH, water, 18.015 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MSHHWGYGKHNGPEHWHKDF PIAKGERQSPVDIDTHTAKY DPSLKPLSVSYDQATSLRIL NNGHAFNVEFDDSQDKAVLK GGPLDGTYRLIQFHFHWGSL DGQGSEHTVDKKKYAAELHL VHWNTKYGDFGKAVQQPDGL AVLGIFLKVGSAKPGLQKVV DVLDSIKTKGKSADFTNFDP RGLLPESLDYWTYPGSLTTP PLLECVTWIVLKEPISVSSE QVLKFRKLNFNGEGEPEELM VDNWRPAQPLKNRQIKASFK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	1006
15N chemical shifts	263
1H chemical shifts	1000

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	entity_3	3

Entities:

Entity 1, entity_1 260 residues - 29289.062 Da.

1	MET	SER	HIS	HIS	TRP	GLY	TYR	GLY	LYS	HIS
2	ASN	GLY	PRO	GLU	HIS	TRP	HIS	LYS	ASP	PHE
3	PRO	ILE	ALA	LYS	GLY	GLU	ARG	GLN	SER	PRO
4	VAL	ASP	ILE	ASP	THR	HIS	THR	ALA	LYS	TYR
5	ASP	PRO	SER	LEU	LYS	PRO	LEU	SER	VAL	SER
6	TYR	ASP	GLN	ALA	THR	SER	LEU	ARG	ILE	LEU
7	ASN	ASN	GLY	HIS	ALA	PHE	ASN	VAL	GLU	PHE
8	ASP	ASP	SER	GLN	ASP	LYS	ALA	VAL	LEU	LYS
9	GLY	GLY	PRO	LEU	ASP	GLY	THR	TYR	ARG	LEU
10	ILE	GLN	PHE	HIS	PHE	HIS	TRP	GLY	SER	LEU
11	ASP	GLY	GLN	GLY	SER	GLU	HIS	THR	VAL	ASP
12	LYS	LYS	LYS	TYR	ALA	ALA	GLU	LEU	HIS	LEU
13	VAL	HIS	TRP	ASN	THR	LYS	TYR	GLY	ASP	PHE
14	GLY	LYS	ALA	VAL	GLN	GLN	PRO	ASP	GLY	LEU
15	ALA	VAL	LEU	GLY	ILE	PHE	LEU	LYS	VAL	GLY
16	SER	ALA	LYS	PRO	GLY	LEU	GLN	LYS	VAL	VAL
17	ASP	VAL	LEU	ASP	SER	ILE	LYS	THR	LYS	GLY
18	LYS	SER	ALA	ASP	PHE	THR	ASN	PHE	ASP	PRO
19	ARG	GLY	LEU	LEU	PRO	GLU	SER	LEU	ASP	TYR
20	TRP	THR	TYR	PRO	GLY	SER	LEU	THR	THR	PRO
21	PRO	LEU	LEU	GLU	CYS	VAL	THR	TRP	ILE	VAL
22	LEU	LYS	GLU	PRO	ILE	SER	VAL	SER	SER	GLU
23	GLN	VAL	LEU	LYS	PHE	ARG	LYS	LEU	ASN	PHE
24	ASN	GLY	GLU	GLY	GLU	PRO	GLU	GLU	LEU	MET
25	VAL	ASP	ASN	TRP	ARG	PRO	ALA	GLN	PRO	LEU
26	LYS	ASN	ARG	GLN	ILE	LYS	ALA	SER	PHE	LYS

Entity 2, entity_2 - Zn - 65.409 Da.

1

ZN

Entity 3, entity_3 - 18.015 Da.

1

HOH

Samples:

sample_1: hCAII 13C 15N, [U-13C; U-15N], 0.5 mM; hCAII 13C 15N 2H, [U-13C; U-15N]2H, 0.5 mM; hCAII 15N, [U-100% 15N], 0.6 mM; hCAII 13C, [U-100% 13C], 0.6 mM; hCAII 1 mM

sample_2: hCAII 13C 15N, [U-100% 13C; U-100% 15N], 0.5 mM; hCAII 13C 15N 2H, [U-13C; U-15N; U-2H], 0.6 mM; hCAII 15N, [U-99% 15N], 0.5 mM; hCAII 99% 13C 15N, [U-99% 13C; U-99% 15N], 0.5 mM; hCAII 10% 13C, [U-10% 13C], 0.6 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_2
3D HNCA	sample_2	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

ARIA v2.3, Linge, O'Donoghue and Nilges - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

TopSpin, Bruker Biospin - processing

CcpNmr Analysis, CCPN - peak picking

NMR spectrometers:

Bruker AvanceIII 800 MHz
Bruker AvanceIII 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	MET	SER	HIS	HIS	TRP	GLY	TYR	GLY	LYS	HIS
2	ASN	GLY	PRO	GLU	HIS	TRP	HIS	LYS	ASP	PHE
3	PRO	ILE	ALA	LYS	GLY	GLU	ARG	GLN	SER	PRO
4	VAL	ASP	ILE	ASP	THR	HIS	THR	ALA	LYS	TYR
5	ASP	PRO	SER	LEU	LYS	PRO	LEU	SER	VAL	SER
6	TYR	ASP	GLN	ALA	THR	SER	LEU	ARG	ILE	LEU
7	ASN	ASN	GLY	HIS	ALA	PHE	ASN	VAL	GLU	PHE
8	ASP	ASP	SER	GLN	ASP	LYS	ALA	VAL	LEU	LYS
9	GLY	GLY	PRO	LEU	ASP	GLY	THR	TYR	ARG	LEU
10	ILE	GLN	PHE	HIS	PHE	HIS	TRP	GLY	SER	LEU
11	ASP	GLY	GLN	GLY	SER	GLU	HIS	THR	VAL	ASP
12	LYS	LYS	LYS	TYR	ALA	ALA	GLU	LEU	HIS	LEU
13	VAL	HIS	TRP	ASN	THR	LYS	TYR	GLY	ASP	PHE
14	GLY	LYS	ALA	VAL	GLN	GLN	PRO	ASP	GLY	LEU
15	ALA	VAL	LEU	GLY	ILE	PHE	LEU	LYS	VAL	GLY
16	SER	ALA	LYS	PRO	GLY	LEU	GLN	LYS	VAL	VAL
17	ASP	VAL	LEU	ASP	SER	ILE	LYS	THR	LYS	GLY
18	LYS	SER	ALA	ASP	PHE	THR	ASN	PHE	ASP	PRO
19	ARG	GLY	LEU	LEU	PRO	GLU	SER	LEU	ASP	TYR
20	TRP	THR	TYR	PRO	GLY	SER	LEU	THR	THR	PRO
21	PRO	LEU	LEU	GLU	CYS	VAL	THR	TRP	ILE	VAL
22	LEU	LYS	GLU	PRO	ILE	SER	VAL	SER	SER	GLU
23	GLN	VAL	LEU	LYS	PHE	ARG	LYS	LEU	ASN	PHE
24	ASN	GLY	GLU	GLY	GLU	PRO	GLU	GLU	LEU	MET
25	VAL	ASP	ASN	TRP	ARG	PRO	ALA	GLN	PRO	LEU
26	LYS	ASN	ARG	GLN	ILE	LYS	ALA	SER	PHE	LYS

1	MET	SER	HIS	HIS	TRP	GLY	TYR	GLY	LYS	HIS
2	ASN	GLY	PRO	GLU	HIS	TRP	HIS	LYS	ASP	PHE
3	PRO	ILE	ALA	LYS	GLY	GLU	ARG	GLN	SER	PRO
4	VAL	ASP	ILE	ASP	THR	HIS	THR	ALA	LYS	TYR
5	ASP	PRO	SER	LEU	LYS	PRO	LEU	SER	VAL	SER
6	TYR	ASP	GLN	ALA	THR	SER	LEU	ARG	ILE	LEU
7	ASN	ASN	GLY	HIS	ALA	PHE	ASN	VAL	GLU	PHE
8	ASP	ASP	SER	GLN	ASP	LYS	ALA	VAL	LEU	LYS
9	GLY	GLY	PRO	LEU	ASP	GLY	THR	TYR	ARG	LEU
10	ILE	GLN	PHE	HIS	PHE	HIS	TRP	GLY	SER	LEU
11	ASP	GLY	GLN	GLY	SER	GLU	HIS	THR	VAL	ASP
12	LYS	LYS	LYS	TYR	ALA	ALA	GLU	LEU	HIS	LEU
13	VAL	HIS	TRP	ASN	THR	LYS	TYR	GLY	ASP	PHE
14	GLY	LYS	ALA	VAL	GLN	GLN	PRO	ASP	GLY	LEU
15	ALA	VAL	LEU	GLY	ILE	PHE	LEU	LYS	VAL	GLY
16	SER	ALA	LYS	PRO	GLY	LEU	GLN	LYS	VAL	VAL
17	ASP	VAL	LEU	ASP	SER	ILE	LYS	THR	LYS	GLY
18	LYS	SER	ALA	ASP	PHE	THR	ASN	PHE	ASP	PRO
19	ARG	GLY	LEU	LEU	PRO	GLU	SER	LEU	ASP	TYR
20	TRP	THR	TYR	PRO	GLY	SER	LEU	THR	THR	PRO
21	PRO	LEU	LEU	GLU	CYS	VAL	THR	TRP	ILE	VAL
22	LEU	LYS	GLU	PRO	ILE	SER	VAL	SER	SER	GLU
23	GLN	VAL	LEU	LYS	PHE	ARG	LYS	LEU	ASN	PHE
24	ASN	GLY	GLU	GLY	GLU	PRO	GLU	GLU	LEU	MET
25	VAL	ASP	ASN	TRP	ARG	PRO	ALA	GLN	PRO	LEU
26	LYS	ASN	ARG	GLN	ILE	LYS	ALA	SER	PHE	LYS

1	MET	SER	HIS	HIS	TRP	GLY	TYR	GLY	LYS	HIS
2	ASN	GLY	PRO	GLU	HIS	TRP	HIS	LYS	ASP	PHE
3	PRO	ILE	ALA	LYS	GLY	GLU	ARG	GLN	SER	PRO
4	VAL	ASP	ILE	ASP	THR	HIS	THR	ALA	LYS	TYR
5	ASP	PRO	SER	LEU	LYS	PRO	LEU	SER	VAL	SER
6	TYR	ASP	GLN	ALA	THR	SER	LEU	ARG	ILE	LEU
7	ASN	ASN	GLY	HIS	ALA	PHE	ASN	VAL	GLU	PHE
8	ASP	ASP	SER	GLN	ASP	LYS	ALA	VAL	LEU	LYS
9	GLY	GLY	PRO	LEU	ASP	GLY	THR	TYR	ARG	LEU
10	ILE	GLN	PHE	HIS	PHE	HIS	TRP	GLY	SER	LEU
11	ASP	GLY	GLN	GLY	SER	GLU	HIS	THR	VAL	ASP
12	LYS	LYS	LYS	TYR	ALA	ALA	GLU	LEU	HIS	LEU
13	VAL	HIS	TRP	ASN	THR	LYS	TYR	GLY	ASP	PHE
14	GLY	LYS	ALA	VAL	GLN	GLN	PRO	ASP	GLY	LEU
15	ALA	VAL	LEU	GLY	ILE	PHE	LEU	LYS	VAL	GLY
16	SER	ALA	LYS	PRO	GLY	LEU	GLN	LYS	VAL	VAL
17	ASP	VAL	LEU	ASP	SER	ILE	LYS	THR	LYS	GLY
18	LYS	SER	ALA	ASP	PHE	THR	ASN	PHE	ASP	PRO
19	ARG	GLY	LEU	LEU	PRO	GLU	SER	LEU	ASP	TYR
20	TRP	THR	TYR	PRO	GLY	SER	LEU	THR	THR	PRO
21	PRO	LEU	LEU	GLU	CYS	VAL	THR	TRP	ILE	VAL
22	LEU	LYS	GLU	PRO	ILE	SER	VAL	SER	SER	GLU
23	GLN	VAL	LEU	LYS	PHE	ARG	LYS	LEU	ASN	PHE
24	ASN	GLY	GLU	GLY	GLU	PRO	GLU	GLU	LEU	MET
25	VAL	ASP	ASN	TRP	ARG	PRO	ALA	GLN	PRO	LEU
26	LYS	ASN	ARG	GLN	ILE	LYS	ALA	SER	PHE	LYS