2A6C | pdb_00002a6c

CRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REGULATOR (NE_1354) FROM NITROSOMONAS EUROPAEA AT 1.90 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2A6C/pdb

• Classification: TRANSCRIPTION
• Organism(s): Nitrosomonas europaea
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-07-02 Released: 2005-07-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.241 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.210 (DCC) 

Literature

Crystal structure of (np_841403.1) from NITROSOMONAS EUROPAEA at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

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

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 19.73 kDa 
• Atom Count: 1,291 
• Modeled Residue Count: 152 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helix-turn-helix motif	A, B	83	Nitrosomonas europaea	Mutation(s): 5  Gene Names: np_841403.1
UniProt
Find proteins for Q82UW4 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82UW4  Go to UniProtKB:  Q82UW4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A]	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:  0.241 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.210 (DCC) 

Diffraction Data: https://doi.org/10.18430/M32A6C

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.862	α = 90
b = 40.788	β = 119.83
c = 53.393	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-07-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary