4Q4U

TvNiR in complex with sulfite, low dose data set


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray-induced changes in the active site structure of octaheme cytochrome c nitrite reductase and its substrate complexes

Lazarenko, V.A.Polyakov, K.M.Trofimov, A.A.Popov, A.N.Tikhonova, T.V.Tikhonov, A.V.Popov, V.O.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eight-heme nitrite reductase
A, B
521Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2)Mutation(s): 0 
Gene Names: nir
EC: 1.7.2.2
Find proteins for L0DSL2 (Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2))
Go to UniProtKB:  L0DSL2
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO3
Query on SO3

Download SDF File 
Download CCD File 
A, B
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

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Download CCD File 
A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.158 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 195.140α = 90.00
b = 195.140β = 90.00
c = 195.140γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description