3SQD | pdb_00003sqd

Crystal structure of human PTIP BRCT5/6-gamma H2AX complex

PDB DOI: https://doi.org/10.2210/pdb3SQD/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-05 Released: 2011-11-09
Deposition Author(s): Yan, W., Shao, Z.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.248 (Depositor), 0.242 (DCC)
R-Value Work:
0.197 (Depositor), 0.195 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of human PTIP BRCT5/6-gamma H2AX

Yan, W., Shao, Z.H.

To be published.

Macromolecule Content

Total Structure Weight: 52.76 kDa
Atom Count: 3,741
Modeled Residue Count: 430
Deposited Residue Count: 458
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PAX-interacting protein 1	A, B	219	Homo sapiens	Mutation(s): 0 Gene Names: PTIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZW49 (Homo sapiens) Explore Q6ZW49 Go to UniProtKB: Q6ZW49
PHAROS: Q6ZW49 GTEx: ENSG00000157212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6ZW49
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.x	C, D	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P16104 (Homo sapiens) Explore P16104 Go to UniProtKB: P16104
PHAROS: P16104 GTEx: ENSG00000188486
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16104
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	C, D	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.248 (Depositor), 0.242 (DCC)
R-Value Work: 0.197 (Depositor), 0.195 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.973	α = 90
b = 101.812	β = 90
c = 61.815	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2017-11-08
Changes: Advisory, Refinement description
Version 1.2: 2023-11-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

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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.