1VPH | pdb_00001vph

CRYSTAL STRUCTURE OF a YbjQ-like protein of unknown function (SSO2532) FROM SULFOLOBUS SOLFATARICUS P2 AT 1.76 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1VPH/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Saccharolobus solfataricus P2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-11-03 Released: 2004-11-16
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.222 (Depositor), 0.230 (DCC)
R-Value Work:
0.189 (Depositor), 0.200 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein (13815834) from Sulfolobus solfataricus at 1.76 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 103.64 kDa
Atom Count: 7,049
Modeled Residue Count: 838
Deposited Residue Count: 894
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein SSO2532	A, B, C, D, E A, B, C, D, E, F	149	Saccharolobus solfataricus P2	Mutation(s): 0
UniProt
Find proteins for Q97VS8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97VS8 Go to UniProtKB: Q97VS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97VS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth B] L [auth C] M [auth C] H [auth A], I [auth A], J [auth B], L [auth C], M [auth C], P [auth D], Q [auth D], R [auth D], T [auth E], V [auth F], W [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain G [auth A] MOL2 format, chain U [auth F] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] mmCIF format, chain U [auth F] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A]	G [auth A], K [auth C], O [auth D], U [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth C] Focus chain O [auth D] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth C] Focus chain O [auth D] Focus chain U [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.222 (Depositor), 0.230 (DCC)
R-Value Work: 0.189 (Depositor), 0.200 (DCC)
R-Value Observed: 0.191 (Depositor)

Diffraction Data: https://doi.org/10.18430/M31VPH

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.86	α = 90
b = 92.18	β = 90
c = 114.13	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-11-16

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-11-16
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2023-09-20
Changes: Data collection, Refinement description