3QNK

Crystal structure of a SusD-like protein (BF3747) from Bacteroides fragilis NCTC 9343 at 2.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb3QNK/pdb

Classification: STRUCTURAL GENOMICS
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-02-08 Released: 2011-03-09
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.211
R-Value Work: 0.183
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Hypothetical SusD-like protein (BF3747) from Bacteroides fragilis NCTC 9343 at 2.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 244.08 kDa
Atom Count: 16,607
Modelled Residue Count: 2,050
Deposited Residue Count: 2,068
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, B, C, D	517	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF3747
UniProt
Find proteins for Q5L904 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5L904 Go to UniProtKB: Q5L904
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5L904
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain M [auth C] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth C]	F [auth B] G [auth B] H [auth B] K [auth C] L [auth C] F [auth B], G [auth B], H [auth B], K [auth C], L [auth C], M [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D]	I [auth B] J [auth B] N [auth C] O [auth C] P [auth C] I [auth B], J [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.211
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 3₁ 2 1
Diffraction Data: https://doi.org/10.18430/M33QNK

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.653	α = 90
b = 146.653	β = 90
c = 226.178	γ = 120

Software Package:

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