7Y37 | pdb_00007y37

Structure of a triple-helix region of human collagen type V

PDB DOI: https://doi.org/10.2210/pdb7Y37/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: synthetic construct
Mutation(s): No

Deposited: 2022-06-10 Released: 2023-07-05
Deposition Author(s): Zhu, Y., Yang, X., Sun, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.183 (Depositor), 0.176 (DCC)
R-Value Work:
0.156 (Depositor), 0.148 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Y37

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

Literature

Structure of a triple-helix region of human collagen type V

Zhu, Y., Yang, X., Sun, F.

To be published.

Macromolecule Content

Total Structure Weight: 7.59 kDa
Atom Count: 735
Modeled Residue Count: 87
Deposited Residue Count: 87
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A triple-helix region of human collagen type V	A, B, C	29	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20908 (Homo sapiens) Explore P20908 Go to UniProtKB: P20908
PHAROS: P20908 GTEx: ENSG00000130635
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20908
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	A, B, C	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.183 (Depositor), 0.176 (DCC)
R-Value Work: 0.156 (Depositor), 0.148 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.865	α = 90
b = 23.675	β = 100.19
c = 36.648	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.