4QEY | pdb_00004qey

Crystal structure of a DUF4425 family protein (BACOVA_05332) from Bacteroides ovatus ATCC 8483 at 2.52 A resolution

PDB DOI: https://doi.org/10.2210/pdb4QEY/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacteroides ovatus ATCC 8483
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-19 Released: 2014-07-16
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.221 (Depositor), 0.223 (DCC)
R-Value Work:
0.196 (Depositor), 0.202 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a hypothetical protein (BACOVA_05332) from Bacteroides ovatus ATCC 8483 at 2.52 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 145.29 kDa
Atom Count: 9,789
Modeled Residue Count: 1,243
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	132	Bacteroides ovatus ATCC 8483	Mutation(s): 0 Gene Names: BACOVA_05332

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain JA [auth H] MOL2 format, chain JA [auth H] mmCIF format, chain JA [auth H]	JA [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain JA [auth H] Interactions & Density Focus chain JA [auth H]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain R [auth B] SDF format, chain NA [auth J] SDF format, chain MA [auth I] SDF format, chain K [auth A] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain R [auth B] MOL2 format, chain NA [auth J] MOL2 format, chain MA [auth I] MOL2 format, chain K [auth A] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain R [auth B] mmCIF format, chain NA [auth J] mmCIF format, chain MA [auth I] mmCIF format, chain K [auth A]	K [auth A] MA [auth I] NA [auth J] R [auth B] W [auth D] K [auth A], MA [auth I], NA [auth J], R [auth B], W [auth D], Y [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain R [auth B] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain K [auth A] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain R [auth B] Focus chain W [auth D] Focus chain Y [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain KA [auth H] SDF format, chain P [auth A] SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth B] SDF format, chain SA [auth J] SDF format, chain S [auth B] SDF format, chain RA [auth J] SDF format, chain QA [auth J] SDF format, chain Q [auth A] SDF format, chain PA [auth J] SDF format, chain OA [auth J] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth H] SDF format, chain L [auth A] SDF format, chain HA [auth G] SDF format, chain GA [auth G] SDF format, chain FA [auth F] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] SDF format, chain AA [auth E] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth J] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth J] MOL2 format, chain OA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain IA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth J] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth J] mmCIF format, chain OA [auth J] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] EA [auth E] AA [auth E], BA [auth E], CA [auth E], DA [auth E], EA [auth E], FA [auth F], GA [auth G], HA [auth G], IA [auth G], KA [auth H], L [auth A], LA [auth H], M [auth A], N [auth A], O [auth A], OA [auth J], P [auth A], PA [auth J], Q [auth A], QA [auth J], RA [auth J], S [auth B], SA [auth J], T [auth B], U [auth C], V [auth C], X [auth D], Z [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain P [auth A] Focus chain PA [auth J] Focus chain Q [auth A] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain S [auth B] Focus chain SA [auth J] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain P [auth A] Focus chain PA [auth J] Focus chain Q [auth A] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain S [auth B] Focus chain SA [auth J] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.221 (Depositor), 0.223 (DCC)
R-Value Work: 0.196 (Depositor), 0.202 (DCC)
R-Value Observed: 0.198 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.59	α = 90
b = 101.34	β = 107.91
c = 91.42	γ = 90

Software Package:

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