1RTT | pdb_00001rtt

Crystal structure determination of a putative NADH-dependent reductase using sulfur anomalous signal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 
    0.228 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1RTT

This is version 1.4 of the entry. See complete history

Literature

Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal.

Agarwal, R.Bonanno, J.B.Burley, S.K.Swaminathan, S.

(2006) Acta Crystallogr D Biol Crystallogr 62: 383-391

  • DOI: https://doi.org/10.1107/S0907444906001600
  • Primary Citation Related Structures: 
    1RTT, 1X77

  • PubMed Abstract: 

    The availability of high-intensity synchrotron facilities, technological advances in data-collection techniques and improved data-reduction and crystallographic software have ushered in a new era in high-throughput macromolecular crystallography. Here, the de novo automated crystal structure determination at 1.28 A resolution of an NAD(P)H-dependent FMN reductase flavoprotein from Pseudomonas aeruginosa PA01-derived protein Q9I4D4 using the anomalous signal from an unusually small number of S atoms is reported. Although this protein lacks the flavodoxin key fingerprint motif [(T/S)XTGXT], it has been confirmed to bind flavin mononucleotide and the binding site was identified via X-ray crystallography. This protein contains a novel flavin mononucleotide-binding site GSLRSGSYN, which has not been previously reported. Detailed statistics pertaining to sulfur phasing and other factors contributing to structure determination are discussed. Structural comparisons of the apoenzyme and the protein complexed with flavin mononucleotide show conformational changes on cofactor binding. NADPH-dependent activity has been confirmed with biochemical assays.


  • Organizational Affiliation
    • Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.

Macromolecule Content 

  • Total Structure Weight: 21.21 kDa 
  • Atom Count: 1,499 
  • Modeled Residue Count: 174 
  • Deposited Residue Count: 193 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
conserved hypothetical protein193Pseudomonas aeruginosa PAO1Mutation(s): 0 
EC: 1
UniProt
Find proteins for Q9I4D4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4D4 
Go to UniProtKB:  Q9I4D4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I4D4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free:  0.228 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.071α = 90
b = 70.386β = 90
c = 85.382γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
HKL-2000data scaling
PHASESphasing
SOLVEphasing
SHARPphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references