BMRB Entry 11451

Name: NMR strucure of stereo-array isotope labelled (SAIL) peptidyl-prolyl cis-trans isomerase from E. coli (EPPIb)
Published: 2015-06-26

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PDB ID: 2rs4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR11451
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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:

NMR strucure of stereo-array isotope labelled (SAIL) peptidyl-prolyl cis-trans isomerase from E. coli (EPPIb)

Deposition date:

2011-07-16

Original release date:

2015-06-26

Authors:

Takeda, Mitsuhiro; Jee, JunGoo; Ono, Akira; Okuma, Kosuke; Terauchi, Tsutomu; Kainosho, Masatsune

Citation:

Citation: Takeda, Mitsuhiro; Jee, JunGoo; Ono, Akira; Terauchi, Tsutomu; Kainosho, Masatsune. "Hydrogen exchange study on the hydroxyl groups of serine and threonine residues in proteins and structure refinement using NOE restraints with polar side-chain groups" J. Am. Chem. Soc. 133, 17420-17427 (2011).
PubMed: 21955241

Assembly members:

Assembly members:
entity, polymer, 164 residues, 18174.578 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: Escherichia coli Vector: pET3a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MVTFHTNHGDIVIKTFDDKA PETVKNFLDYCREGFYNNTI FHRVINGFMIQGGGFEPGMK QKATKEPIKNEANNGLKNTR GTLAMARTQAPHSATAQFFI NVVDNDFLNFSGESLQGWGY CVFAEVVDGMDVVDKIKGVA TGRSGMHQDVPKEDVIIESV TVSE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	497
15N chemical shifts	173
1H chemical shifts	858

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	peptidyl-prolyl cis-trans isomerase	1

Entities:

Entity 1, peptidyl-prolyl cis-trans isomerase 164 residues - 18174.578 Da.

1

MET

VAL

THR

PHE

HIS

THR

ASN

HIS

GLY

ASP

2

ILE

VAL

ILE

LYS

THR

PHE

ASP

LYS

ALA

3

PRO

GLU

THR

VAL

LYS

ASN

PHE

LEU

ASP

TYR

4

CYS

ARG

GLU

GLY

PHE

TYR

ASN

THR

ILE

5

PHE

HIS

ARG

VAL

ILE

ASN

GLY

PHE

MET

ILE

6

GLN

GLY

PHE

GLU

PRO

GLY

MET

LYS

7

GLN

LYS

ALA

THR

LYS

GLU

PRO

ILE

LYS

ASN

8

GLU

ALA

ASN

GLY

LEU

LYS

ASN

THR

ARG

9

GLY

THR

LEU

ALA

MET

ALA

ARG

THR

GLN

ALA

10

PRO

HIS

SER

ALA

THR

ALA

GLN

PHE

ILE

11

ASN

VAL

ASP

ASN

ASP

PHE

LEU

ASN

PHE

12

SER

GLY

GLU

SER

LEU

GLN

GLY

TRP

GLY

TYR

13

CYS

VAL

PHE

ALA

GLU

VAL

ASP

GLY

MET

14

ASP

VAL

ASP

LYS

ILE

LYS

GLY

VAL

ALA

15

THR

GLY

ARG

SER

GLY

MET

HIS

GLN

ASP

VAL

16

PRO

LYS

GLU

ASP

VAL

ILE

GLU

SER

VAL

17

THR

VAL

SER

GLU

Samples:

sample_1: EPPIb, SAIL [e-SAIL Phe, e-SAIL Tyr], 0.3 mM; sodium phosphate 50 mM; DTT 1 mM; sodium chloride 100 mM

sample_2: EPPIb, SAIL [z-SAIL Phe, e-SAIL Tyr], 0.3 mM; sodium phosphate 50 mM; DTT 1 mM; sodium chloride 100 mM

sample_3: EPPIb, SAIL [d-SAIL Phe, d-SAIL Tyr], 0.3 mM; sodium phosphate 50 mM; DTT 1 mM; sodium chloride 100 mM

sample_conditions_1: ionic strength: 0.4 M; pH: 6.2; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
2D HB(CBCG)HE	sample_1	isotropic	sample_conditions_1
2D HB(CBCGCZ) HZ	sample_2	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker DRX 800 MHz

PDB	1LOP 2NUL 2RS4
DBJ	BAB34010 BAE76302 BAG76074 BAI23892 BAI29364
EMBL	CAD05020 CAP75055 CAQ30997 CAQ88114 CAQ97399
GB	AAA23453 AAC73627 AAG54882 AAL19490 AAN42110
PIR	AB0569
REF	NP_308614 NP_415058 NP_455128 NP_459531 NP_706403
SP	P23869
AlphaFold	P23869