1ZX5 | pdb_00001zx5

The structure of a putative mannosephosphate isomerase from Archaeoglobus fulgidus

• PDB DOI: https://doi.org/10.2210/pdb1ZX5/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-06 Released: 2005-07-19 
• Deposition Author(s): Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.191 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

The structure of a putative mannosephosphate isomerase from Archaeoglobus fulgidus

Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.54 kDa 
• Atom Count: 2,710 
• Modeled Residue Count: 300 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mannosephosphate isomerase, putative	A	300	Archaeoglobus fulgidus	Mutation(s): 4  Gene Names: AF0035 EC: 5.3.1.8
UniProt
Find proteins for O30200 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O30200  Go to UniProtKB:  O30200

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LFR	B [auth A]	beta-L-fructofuranose C6 H12 O6 RFSUNEUAIZKAJO-AZGQCCRYSA-N
GOL	K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.191 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.045	α = 90
b = 160.045	β = 90
c = 160.045	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-19 
Deposition Author(s): Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary