BMRB Entry 19229

Name: PHD Domain from Human SHPRH
Published: 2013-08-12

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PDB ID: 2m85
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19229
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

PHD Domain from Human SHPRH

Deposition date:

2013-05-07

Original release date:

2013-08-12

Authors:

Machado, Luciana; Pustovalova, Yulia; Pozhidaeva, Alexandra; Almeida, Fabio; Bezsonova, Irina; Korzhnev, Dmitry

Citation:

Citation: Machado, Luciana; Pustovalova, Yulia; Kile, Andrew; Pozhidaeva, Alexandra; Cimprich, Karlene; Almeida, Fabio; Bezsonova, Irina; Korzhnev, Dmitry. "PHD domain from human SHPRH." J. Biomol. NMR 56, 393-399 (2013).
PubMed: 23907177

Assembly members:

Assembly members:
SHPRH, polymer, 73 residues, 7776.120 Da.
ZINC ION, non-polymer, 65.409 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 Vector: PGEX-4T3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SHPRH: GSPNSRVDFNTSDYRFECIC GELDQIDRKPRVQCLKCHLW QHAKCVNYDEKNLKIKPFYC PHCLVAMEPVSTR

Data sets:

assigned_chemical_shifts
- SHPRH_cshifts

Data type	Count
13C chemical shifts	285
15N chemical shifts	68
1H chemical shifts	467

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SHPRH	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, SHPRH 73 residues - 7776.120 Da.

1

GLY

SER

PRO

ASN

SER

ARG

VAL

ASP

PHE

ASN

2

THR

SER

ASP

TYR

ARG

PHE

GLU

CYS

ILE

CYS

3

GLY

GLU

LEU

ASP

GLN

ILE

ASP

ARG

LYS

PRO

4

ARG

VAL

GLN

CYS

LEU

LYS

CYS

HIS

LEU

TRP

5

GLN

HIS

ALA

LYS

CYS

VAL

ASN

TYR

ASP

GLU

6

LYS

ASN

LEU

LYS

ILE

LYS

PRO

PHE

TYR

CYS

7

PRO

HIS

CYS

LEU

VAL

ALA

MET

GLU

PRO

VAL

8

SER

THR

ARG

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: HEPES, [U-100% 13C; U-100% 15N], 50 mM; sodium chloride 150 mM; ZINC ION 0.05 mM; DTT 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 150 mM; pH: 7.0; pressure: 1 atm; temperature: 293 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 HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	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 CCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CARA v1.8, Keller and Wuthrich - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS v2.2, Cornilescu, Delaglio and Bax - prediction of backbone torsion angles

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

ABACUS v2.5, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization

Molmol v2K.2, Koradi, Billeter and Wuthrich - data analysis

CNS v2.5, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization

NMR spectrometers:

Varian Avance 500 MHz
Varian Avance 800 MHz

PDB	2M85
REF	XP_002747128 XP_010335830 XP_010335831 XP_012308223 XP_012308230