6MU0 | pdb_00006mu0

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.149 (Depositor), 0.149 (DCC)
R-Value Work:
0.134 (Depositor), 0.134 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47636
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5RP (Subject of Investigation/LOI) Query on 5RP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RIBULOSE-5-PHOSPHATE C₅ H₁₁ O₈ P FNZLKVNUWIIPSJ-UHNVWZDZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on 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 (Depositor), 0.149 (DCC)
R-Value Work: 0.134 (Depositor), 0.134 (DCC)
R-Value Observed: 0.135 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

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

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Entry History

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.