6MU0

Crystal Structure of Ribose-5-phosphate Isomerase B from Mycoplasma genitalium with bound Ribulose-5-phosphate

• PDB DOI: https://doi.org/10.2210/pdb6MU0/pdb

• Classification: ISOMERASE
• Organism(s): Mycoplasmoides genitalium G37
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-22 Released: 2018-11-14 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.149 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 

Starting Model: experimental

Literature

Crystal Structure of Ribose-5-phosphate Isomerase B from Mycoplasma genitalium with bound Ribulose-5-phosphate

Dranow, D.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.21 kDa 
• Atom Count: 1,447 
• Modelled Residue Count: 152 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ribose-5-phosphate isomerase B	A	160	Mycoplasmoides genitalium G37	Mutation(s): 0  Gene Names: rpiB, MG396 EC: 5.3.1.6
UniProt
Find proteins for P47636 (Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37)) Explore P47636  Go to UniProtKB:  P47636

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5RP (Subject of Investigation/LOI)	B [auth A]	RIBULOSE-5-PHOSPHATE C5 H11 O8 P FNZLKVNUWIIPSJ-UHNVWZDZSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.149 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/m36mu0

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.35	α = 90
b = 45.35	β = 90
c = 138.51	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary