1QWR | pdb_00001qwr

Crystal Structure Analysis of the Mannose 6-Phosphate Isomerase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1QWR/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-09-03 Released: 2004-03-02 
• Deposition Author(s): Kim, Y., Lezondra, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.232 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Crystal structure analysis of the mannose 6-phosphate isomerase from Bacillus subtilis

Kim, Y., Lezondra, L., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.29 kDa 
• Atom Count: 5,683 
• Modeled Residue Count: 629 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose-6-phosphate isomerase	A, B	319	Bacillus subtilis	Mutation(s): 3  Gene Names: PMI OR BSU35790 EC: 5.3.1.8
UniProt
Find proteins for P39841 (Bacillus subtilis (strain 168)) Explore P39841  Go to UniProtKB:  P39841

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-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: 1.80 Å
• R-Value Free:  0.232 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.116	α = 90
b = 72.534	β = 91.89
c = 70.309	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-02 
Deposition Author(s): Kim, Y., Lezondra, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-03-02
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary