3EHQ | pdb_00003ehq

Crystal Structure of Human Osteoclast Stimulating Factor

PDB DOI: https://doi.org/10.2210/pdb3EHQ/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-09-14 Released: 2009-08-04
Deposition Author(s): Tong, S., Zhou, H., Gao, Y., Zhu, Z., Zhang, X., Teng, M., Niu, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.284 (Depositor), 0.286 (DCC)
R-Value Work:
0.210 (Depositor), 0.213 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3EHQ

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

Literature

Crystal structure of human osteoclast stimulating factor

Tong, S., Zhou, H., Gao, Y., Zhu, Z., Zhang, X., Teng, M., Niu, L.

(2009) Proteins 75: 245-251

PubMed: 19137598 Search on PubMed
DOI: https://doi.org/10.1002/prot.22333
Primary Citation Related Structures:
3EHQ, 3EHR

Organizational Affiliation

Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.

Macromolecule Content

Total Structure Weight: 50.11 kDa
Atom Count: 2,923
Modeled Residue Count: 363
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Osteoclast-stimulating factor 1	A, B	222	Homo sapiens	Mutation(s): 1 Gene Names: OSTF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92882 (Homo sapiens) Explore Q92882 Go to UniProtKB: Q92882
PHAROS: Q92882 GTEx: ENSG00000134996
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92882
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.284 (Depositor), 0.286 (DCC)
R-Value Work: 0.210 (Depositor), 0.213 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.057	α = 90
b = 56.86	β = 90
c = 170.125	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2024-11-20
Changes: Data collection, 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.