2O4X | pdb_00002o4x

Crystal structure of human P100 tudor domain

PDB DOI: https://doi.org/10.2210/pdb2O4X/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2006-12-05 Released: 2007-02-13
Deposition Author(s): Shaw, N., Zhao, M., Cheng, C., Xu, H., Yang, J., Silvennoinen, O., Rao, Z., Wang, B.C., Liu, Z.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.249 (Depositor)
R-Value Work:
0.233 (Depositor)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2O4X

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of human P100 tudor domain

Shaw, N., Zhao, M., Cheng, C., Xu, H., Yang, J., Silvennoinen, O., Rao, Z., Wang, B.C., Liu, Z.J.

To be published.

Macromolecule Content

Total Structure Weight: 34.96 kDa
Atom Count: 2,592
Modeled Residue Count: 304
Deposited Residue Count: 308
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal nuclease domain-containing protein 1	A	217	Homo sapiens	Mutation(s): 0 EC: 3.1.31.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZF4 (Homo sapiens) Explore Q7KZF4 Go to UniProtKB: Q7KZF4
PHAROS: Q7KZF4 GTEx: ENSG00000197157
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7KZF4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal nuclease domain-containing protein 1	B	91	Homo sapiens	Mutation(s): 0 EC: 3.1.31.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZF4 (Homo sapiens) Explore Q7KZF4 Go to UniProtKB: Q7KZF4
PHAROS: Q7KZF4 GTEx: ENSG00000197157
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7KZF4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.249 (Depositor)
R-Value Work: 0.233 (Depositor)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.931	α = 90
b = 93.413	β = 90
c = 95.279	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
XFIT	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Silvennoinen, O.

Revision History (Full details and data files)

Version 1.0: 2007-02-13
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.