1O1X

Crystal structure of a ribose 5-phosphate isomerase rpib (tm1080) from thermotoga maritima at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1O1X/pdb

• Classification: ISOMERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-02-12 Released: 2003-04-01 
• 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: 
  0.138 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.117 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.118 (Depositor) 

Literature

Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution.

Xu, Q., Schwarzenbacher, R., McMullan, D., von Delft, F., Brinen, L.S., Canaves, J.M., Dai, X., Deacon, A.M., Elsliger, M.A., Eshagi, S., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S.K., Jaroszewski, L., Karlak, C., Klock, H.E., Koesema, E., Kovarik, J.S., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Page, R., Quijano, K., Robb, A., Spraggon, G., Stevens, F., van den Bedem, H., Velasquez, J., Vincent, J., Wang, X., West, B., Wolf, G., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2004) Proteins 56: 171-175

• PubMed: 15162497 
• DOI: https://doi.org/10.1002/prot.20129
• Primary Citation of Related Structures:  
  1O1X

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Organizational Affiliation: 

The Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 17.63 kDa 
• Atom Count: 1,390 
• Modelled Residue Count: 145 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ribose-5-phosphate isomerase RpiB	A	155	Thermotoga maritima	Mutation(s): 3  Gene Names: TM1080 EC: 5.3.1.6
UniProt
Find proteins for Q9X0G9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0G9  Go to UniProtKB:  Q9X0G9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.138 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.117 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.118 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31O1X

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.49	α = 90
b = 73.89	β = 90
c = 87.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
RESOLVE	model building
SOLVE	phasing
CNS	refinement
MOSFLM	data reduction
XFIT	data reduction
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2003-04-01
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-07-18
  Changes: Data collection, Database references
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2023-01-25
  Changes: Database references, Derived calculations