4FXT | pdb_00004fxt

Crystal structure of a DUF3823 family protein (BACOVA_02663) from Bacteroides ovatus ATCC 8483 at 2.77 A resolution

PDB DOI: https://doi.org/10.2210/pdb4FXT/pdb

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

Deposited: 2012-07-03 Released: 2012-07-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.217 (Depositor), 0.230 (DCC)
R-Value Work:
0.183 (Depositor), 0.200 (DCC)
R-Value Observed:
0.184 (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 (BACOVA_02663) from Bacteroides ovatus ATCC 8483 at 2.77 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 312.14 kDa
Atom Count: 21,144
Modeled Residue Count: 2,715
Deposited Residue Count: 2,828
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, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	202	Bacteroides ovatus ATCC 8483	Mutation(s): 0 Gene Names: BACOVA_02663
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 AA [auth K] SDF format, chain BA [auth L] SDF format, chain CA [auth M] SDF format, chain DA [auth N] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth G] SDF format, chain X [auth H] SDF format, chain Y [auth I] SDF format, chain Z [auth J] MOL2 format, chain AA [auth K] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth M] MOL2 format, chain DA [auth N] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth G] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] mmCIF format, chain AA [auth K] mmCIF format, chain BA [auth L] mmCIF format, chain CA [auth M] mmCIF format, chain DA [auth N] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth G] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J]	AA [auth K] BA [auth L] CA [auth M] DA [auth N] O [auth A] AA [auth K], BA [auth L], CA [auth M], DA [auth N], O [auth A], P [auth B], Q [auth B], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

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, K, L, M, N	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.217 (Depositor), 0.230 (DCC)
R-Value Work: 0.183 (Depositor), 0.200 (DCC)
R-Value Observed: 0.184 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34FXT

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.81	α = 90
b = 351.002	β = 93.42
c = 90.343	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