5YFW

Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP

• PDB DOI: https://doi.org/10.2210/pdb5YFW/pdb

• Classification: ISOMERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-09-22 Released: 2018-02-14 
• Deposition Author(s): Gogoi, P., Kanaujia, S.P.
• Funding Organization(s): Department of Biotechnology (DBT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.213 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 111.57 kDa 
• Atom Count: 8,256 
• Modelled Residue Count: 966 
• Deposited Residue Count: 972 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose 1,5-bisphosphate isomerase	A, B, C	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	E [auth A], H [auth B], L [auth C]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
RI2 (Subject of Investigation/LOI)	D [auth A], G [auth B], K [auth C]	1,5-di-O-phosphono-alpha-D-ribofuranose C5 H12 O11 P2 AAAFZMYJJHWUPN-TXICZTDVSA-N
MRD	J [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
K	F [auth A], I [auth B], M [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RI2	Binding MOAD:  5YFW	Kd: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.213 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.7	α = 90
b = 98.7	β = 90
c = 256.551	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOSFLM	data processing
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Gogoi, P., Kanaujia, S.P.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT)	India	BT/302/NE/TBP/2012 dated 07.01.2013

Revision History  

• 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