3EUA | pdb_00003eua

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (BSU32610) FROM BACILLUS SUBTILIS AT 1.90 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3EUA/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-09 Released: 2008-10-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of yurp protein (np_391141.1) from bacillus subtilis at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 298.98 kDa 
• Atom Count: 22,425 
• Modeled Residue Count: 2,605 
• Deposited Residue Count: 2,632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE FRUCTOSE-AMINOACID-6-PHOSPHATE DEGLYCASE	A, B, C, D, E, F, G, H	329	Bacillus subtilis	Mutation(s): 0  Gene Names: NP_391141.1, BSU32610, yurP EC: 3.5
UniProt
Find proteins for O32157 (Bacillus subtilis (strain 168)) Explore O32157  Go to UniProtKB:  O32157

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	I [auth C], K [auth H]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL	J [auth C], L [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EUA

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.857	α = 109.3
b = 91.822	β = 100.45
c = 119.041	γ = 96.55

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary