5ZC4 | pdb_00005zc4

Crystal Structure of RNF13 RING domain

PDB DOI: https://doi.org/10.2210/pdb5ZC4/pdb

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

Deposited: 2018-02-14 Released: 2019-02-27
Deposition Author(s): Datta, A.B., Sarkar, S.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.186 (Depositor), 0.192 (DCC)
R-Value Work:
0.166 (Depositor), 0.171 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of RNF13 RING domain

Sarkar, S., Datta, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 17.94 kDa
Atom Count: 1,294
Modeled Residue Count: 145
Deposited Residue Count: 152
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF13	A, B [auth D]	76	Homo sapiens	Mutation(s): 0 Gene Names: RNF13, RZF EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O43567 (Homo sapiens) Explore O43567 Go to UniProtKB: O43567
PHAROS: O43567 GTEx: ENSG00000082996
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43567
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth D] SDF format, chain E [auth D] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth D] MOL2 format, chain E [auth D] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth D] mmCIF format, chain E [auth D]	C [auth A], D [auth A], E [auth D], F [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth D] Focus chain F [auth D] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth D] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.186 (Depositor), 0.192 (DCC)
R-Value Work: 0.166 (Depositor), 0.171 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.338	α = 90
b = 90.338	β = 90
c = 45.445	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHELXD	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-02-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	India	500241/Z/11/Z

Revision History (Full details and data files)

Version 1.0: 2019-02-27
Type: Initial release
Version 1.1: 2024-03-27
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.