3B4T | pdb_00003b4t

Crystal structure of Mycobacterium tuberculosis RNase PH, the Mycobacterium tuberculosis Structural Genomics Consortium target Rv1340

• PDB DOI: https://doi.org/10.2210/pdb3B4T/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-24 Released: 2007-11-20 
• Deposition Author(s): Antczak, A.J., Berger, J.M., Lekin, T., Segelke, B.W., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB), TB Structural Genomics Consortium (TBSGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.229 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.203 (DCC) 

Starting Model: experimental

Literature

2.1 A Crystal structure of RNase PH from Mycobacterium tuberculosis.

Antczak, A.J., Lekin, T., Segelke, B.W., Berger, J.M.

To be published.

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: 166.74 kDa 
• Atom Count: 11,806 
• Modeled Residue Count: 1,442 
• Deposited Residue Count: 1,572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease PH	A, B, C, D, E, F	262	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: rph, rphA, Rv1340, MT1381, MTCY130.25, MTCY02B10.04 EC: 2.7.7.56
UniProt
Find proteins for P9WGZ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGZ7  Go to UniProtKB:  P9WGZ7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth A], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D], N [auth E], O [auth F], P [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.229 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.203 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.529	α = 90
b = 152.406	β = 109.46
c = 83.512	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Antczak, A.J., Berger, J.M., Lekin, T., Segelke, B.W., Mycobacterium Tuberculosis Structural Proteomics Project (XMTB), TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary