4PYZ | pdb_00004pyz

Crystal structure of the first two Ubl domains of Deubiquitylase USP7

PDB DOI: https://doi.org/10.2210/pdb4PYZ/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-03-28 Released: 2014-04-16
Deposition Author(s): Walker, J.R., Dong, A., Ong, M.S., Dhe-Paganon, S., Kania, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free:
0.287 (Depositor), 0.307 (DCC)
R-Value Work:
0.244 (Depositor), 0.254 (DCC)
R-Value Observed:
0.245 (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 the first two Ubl domains of Deubiquitylase USP7

Ong, M.S., Walker, J.R., Dong, A., Dhe-Paganon, S., Kania, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 63.47 kDa
Atom Count: 4,106
Modeled Residue Count: 524
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 7	A, B	273	Homo sapiens	Mutation(s): 0 Gene Names: USP7, HAUSP EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens) Explore Q93009 Go to UniProtKB: Q93009
PHAROS: Q93009 GTEx: ENSG00000187555
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93009
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.287 (Depositor), 0.307 (DCC)
R-Value Work: 0.244 (Depositor), 0.254 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.328	α = 90
b = 103.755	β = 90
c = 116.197	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
BUSTER	refinement
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-16

Deposition Author(s):

Dhe-Paganon, S.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-04-16
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-09
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.