4F53 | pdb_00004f53

Crystal structure of a susd homolog (BACOVA_04803) from Bacteroides ovatus ATCC 8483 at 2.25 A resolution

PDB DOI: https://doi.org/10.2210/pdb4F53/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bacteroides ovatus ATCC 8483
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-05-11 Released: 2012-07-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.174 (Depositor), 0.180 (DCC)
R-Value Work:
0.149 (Depositor), 0.150 (DCC)
R-Value Observed:
0.150 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a susd homolog (BACOVA_04803) from Bacteroides ovatus ATCC 8483 at 2.25 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 119.22 kDa
Atom Count: 8,799
Modeled Residue Count: 996
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD homolog	A, B	520	Bacteroides ovatus ATCC 8483	Mutation(s): 0 Gene Names: BACOVA_04803
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [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: 2.25 Å
R-Value Free: 0.174 (Depositor), 0.180 (DCC)
R-Value Work: 0.149 (Depositor), 0.150 (DCC)
R-Value Observed: 0.150 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34F53

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.999	α = 90
b = 226.202	β = 90
c = 62.927	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