3MX3 | pdb_00003mx3

Crystal structure of a SusD homolog (BF0972) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3MX3/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-06 Released: 2010-07-07 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of a SusD homolog (BF0972) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 113.5 kDa 
• Atom Count: 8,617 
• Modeled Residue Count: 940 
• Deposited Residue Count: 980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD homolog	A, B	490	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF0972
UniProt
Find proteins for Q5LGM6 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LGM6  Go to UniProtKB:  Q5LGM6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A], I [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33MX3

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.35	α = 90
b = 87.876	β = 116.66
c = 78.253	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary