3OQQ | pdb_00003oqq

Crystal structure of a Putative lipoprotein (BACOVA_00967) from Bacteroides ovatus at 2.08 A resolution

PDB DOI: https://doi.org/10.2210/pdb3OQQ/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Bacteroides ovatus ATCC 8483
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-03 Released: 2011-09-14
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.204 (Depositor), 0.210 (DCC)
R-Value Work:
0.161 (Depositor), 0.170 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Putative lipoprotein (BACOVA_00967) from Bacteroides ovatus at 2.08 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 49.41 kDa
Atom Count: 3,569
Modeled Residue Count: 411
Deposited Residue Count: 435
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipoprotein	A	435	Bacteroides ovatus ATCC 8483	Mutation(s): 0 Gene Names: BACOVA_00967
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.204 (Depositor), 0.210 (DCC)
R-Value Work: 0.161 (Depositor), 0.170 (DCC)
R-Value Observed: 0.163 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33OQQ

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.64	α = 90
b = 118.58	β = 110.41
c = 49.33	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
BUSTER-TNT	refinement
XSCALE	data processing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing
autoSHARP	phasing
BUSTER	refinement