4HYZ | pdb_00004hyz

Crystal structure of a DUF3887 family protein (RUMGNA_01855) from Ruminococcus gnavus ATCC 29149 at 2.25 A resolution

PDB DOI: https://doi.org/10.2210/pdb4HYZ/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Mediterraneibacter gnavus ATCC 29149
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-14 Released: 2013-01-09
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.208 (Depositor), 0.210 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a hypothetical protein (RUMGNA_01855) from Ruminococcus gnavus ATCC 29149 at 2.25 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 28.37 kDa
Atom Count: 2,029
Modeled Residue Count: 228
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	114	Mediterraneibacter gnavus ATCC 29149	Mutation(s): 0
UniProt
Find proteins for A7B2S7 (Mediterraneibacter gnavus (strain ATCC 29149 / DSM 114966 / JCM 6515 / VPI C7-9)) Explore A7B2S7 Go to UniProtKB: A7B2S7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7B2S7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] K [auth B] L [auth B] M [auth B] C [auth A], D [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] S [auth B] G [auth A], H [auth A], I [auth A], J [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] O [auth B] P [auth B] Q [auth B] E [auth A], F [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [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: 2.25 Å
R-Value Free: 0.208 (Depositor), 0.210 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34HYZ

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.29	α = 90
b = 66.29	β = 90
c = 253.83	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
SHELXD	phasing
BUSTER	refinement