4LAF | pdb_00004laf

Crystal structure of PnpB complex with FMN

• PDB DOI: https://doi.org/10.2210/pdb4LAF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas sp. WBC-3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-19 Released: 2014-06-25 
• Deposition Author(s): Su, J., Zhang, C., Li, N., Gu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal structure of PnpB complex with FMN

Su, J., Zhang, C., Li, N., Gu, L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 90.07 kDa 
• Atom Count: 6,043 
• Modeled Residue Count: 793 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H dehydrogenase (quinone)	A, B, C, D	207	Pseudomonas sp. WBC-3	Mutation(s): 0  Gene Names: pnpB EC: 1.6.5.2 (PDB Primary Data), 1.6.5.6 (UniProt)
UniProt
Find proteins for C1I202 (Pseudomonas sp. (strain WBC-3)) Explore C1I202  Go to UniProtKB:  C1I202

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.553	α = 90
b = 188.553	β = 90
c = 61.203	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Su, J., Zhang, C., Li, N., Gu, L.

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations