2IST | pdb_00002ist

crystal structure of RluD from E. coli

• PDB DOI: https://doi.org/10.2210/pdb2IST/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-18 Released: 2006-10-31 
• Deposition Author(s): Foster, P.G., Finer-Moore, J.S., Stroud, R.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of RluD from E. coli

Foster, P.G., Finer-Moore, J.S., Stroud, R.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.21 kDa 
• Atom Count: 2,838 
• Modeled Residue Count: 321 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal large subunit pseudouridine synthase D	A	325	Escherichia coli	Mutation(s): 0  Gene Names: rluD, sfhB EC: 5.4.99 (PDB Primary Data), 5.4.99.23 (UniProt)
UniProt
Find proteins for P33643 (Escherichia coli (strain K12)) Explore P33643  Go to UniProtKB:  P33643

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCT	C [auth A], D [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.32	α = 90
b = 75.14	β = 90
c = 85.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): Foster, P.G., Finer-Moore, J.S., Stroud, R.M.

Revision History  

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations