3H1W | pdb_00003h1w

Crystal structure of mannose 6-phosphate isomerase bound with zinc and yttrium

• PDB DOI: https://doi.org/10.2210/pdb3H1W/pdb

• Classification: ISOMERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-14 Released: 2009-05-19 
• Deposition Author(s): Sagurthi, S.R., Giri, G., Savithri, H.S., Murthy, M.R.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mannose 6-phosphate isomerase fromSalmonella typhimurium bound to metal atoms and substrate: Implications for catalytic mechanism

Sagurthi, S.R., Giri, G., Savithri, H.S., Murthy, M.R.N.

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)

Macromolecule Content 

• Total Structure Weight: 43.26 kDa 
• Atom Count: 3,229 
• Modeled Residue Count: 390 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose-6-phosphate isomerase	A	393	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: AAL20387, manA, pmi, STM1467 EC: 5.3.1.8
UniProt
Find proteins for P25081 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P25081  Go to UniProtKB:  P25081

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y1	H [auth A]	YTTRIUM ION Y KAJPZYFHSCFBCI-UHFFFAOYSA-N
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.98	α = 90
b = 92.36	β = 90
c = 111.49	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Sagurthi, S.R., Giri, G., Savithri, H.S., Murthy, M.R.N.

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description