4Q88 | pdb_00004q88

Glycosyl hydrolase family 88 from Bacteroides vulgatus

• PDB DOI: https://doi.org/10.2210/pdb4Q88/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-25 Released: 2014-05-21 
• Deposition Author(s): Osipiuk, J., Li, H., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.164 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

Glycosyl hydrolase Family 88 from Bacteroides vulgatus

Osipiuk, J., Li, H., Endres, M., Joachimiak, A.

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 84.74 kDa 
• Atom Count: 6,810 
• Modeled Residue Count: 698 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	359	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_1783
UniProt
Find proteins for A6L195 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L195  Go to UniProtKB:  A6L195

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.73 Å
• R-Value Free:  0.164 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34Q88

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.415	α = 65.3
b = 73.502	β = 83.66
c = 73.183	γ = 90.94

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXCD	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-21 
Deposition Author(s): Osipiuk, J., Li, H., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary