3PET | pdb_00003pet

Crystal structure of a putative adhesin (BF0245) from Bacteroides fragilis NCTC 9343 at 2.07 A resolution

PDB DOI: https://doi.org/10.2210/pdb3PET/pdb

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

Deposited: 2010-10-27 Released: 2011-02-09
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.210 (Depositor), 0.220 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative adhesin (BF0245) from Bacteroides fragilis NCTC 9343 at 2.07 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 49.81 kDa
Atom Count: 3,745
Modeled Residue Count: 436
Deposited Residue Count: 442
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 adhesin	A, B	221	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF0202
UniProt
Find proteins for Q5LIP7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LIP7 Go to UniProtKB: Q5LIP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LIP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain J [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B]	D [auth A], N [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain M [auth B]	C [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [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: 2.07 Å
R-Value Free: 0.210 (Depositor), 0.220 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33PET

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.59	α = 90
b = 60.7	β = 90
c = 205.11	γ = 90

Software Package:

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