5YFS
Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate
- PDB DOI: https://doi.org/10.2210/pdb5YFS/pdb
- Classification: ISOMERASE
- Organism(s): Pyrococcus horikoshii OT3
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2017-09-22 Released: 2018-02-14 
- Funding Organization(s): Department of Biotechnology (DBT)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.198 
- R-Value Work: 0.144 
- R-Value Observed: 0.146 
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Ribose 1,5-bisphosphate isomerase | 324 | Pyrococcus horikoshii OT3 | Mutation(s): 1  Gene Names: PH0208 EC: 5.3.1.29 | ||
UniProt | |||||
Find proteins for O57947 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57947  Go to UniProtKB:  O57947 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O57947 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
RI2 (Subject of Investigation/LOI) Query on RI2 | D [auth A], H [auth B], K [auth C] | 1,5-di-O-phosphono-alpha-D-ribofuranose C5 H12 O11 P2 AAAFZMYJJHWUPN-TXICZTDVSA-N | |||
MPD Query on MPD | G [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N | |||
K Query on K | E [auth A], I [auth B], L [auth C] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
CL Query on CL | F [auth A], J [auth B], M [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.198 
- R-Value Work: 0.144 
- R-Value Observed: 0.146 
- Space Group: P 31 1 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 98.65 | α = 90 |
b = 98.65 | β = 90 |
c = 256.731 | γ = 120 |
Software Name | Purpose |
---|---|
HKL-3000 | data collection |
MOSFLM | data processing |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-02-14  Deposition Author(s): Gogoi, P., Kanaujia, S.P.
Funding Organization | Location | Grant Number |
---|---|---|
Department of Biotechnology (DBT) | India | BT/302/NE/TBP/2012 dated 07.01.2013 |
Revision History (Full details and data files)
- Version 1.0: 2018-02-14
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations - Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary