3RPF | pdb_00003rpf

Protein-protein complex of subunit 1 and 2 of Molybdopterin-converting factor from Helicobacter pylori 26695

• PDB DOI: https://doi.org/10.2210/pdb3RPF/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-26 Released: 2011-06-29 
• Deposition Author(s): Nocek, B., Stein, A., Marshall, N., Jedrzejczak, R., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.242 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Protein-protein complex of subunit 1 and 2 of Molybdopterin-converting factor from Helicobacter pylori 26695

Nocek, B., Stein, A., Marshall, N., Jedrzejczak, R., Babnigg, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.18 kDa 
• Atom Count: 3,448 
• Modeled Residue Count: 428 
• Deposited Residue Count: 444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin synthase catalytic subunit	A, B	148	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: moaE, HP_0800 EC: 2 (PDB Primary Data), 2.8.1.12 (UniProt)
UniProt
Find proteins for P56422 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56422  Go to UniProtKB:  P56422

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin converting factor, subunit 1 (MoaD)	C, D	74	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: HP_0801
UniProt
Find proteins for O25482 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25482  Go to UniProtKB:  O25482

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A], G [auth A], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.242 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.187	α = 90
b = 127.582	β = 90
c = 187.945	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
ARP/wARP	model building
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Nocek, B., Stein, A., Marshall, N., Jedrzejczak, R., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-01-11
  Changes: Structure summary
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary