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- PDB-2v9c: X-ray Crystallographic Structure of a Pseudomonas aeruginosa Azor... -

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Basic information

Entry
Database: PDB / ID: 2v9c
TitleX-ray Crystallographic Structure of a Pseudomonas aeruginosa Azoreductase in Complex with Methyl Red.
ComponentsFMN-DEPENDENT NADH-AZOREDUCTASE 1
KeywordsOXIDOREDUCTASE / FMN / NAD / FLAVODOXIN / FLAVOPROTEIN / NADPH-DEPENDENT / FLAVIN MONONUCLEOTIDE
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / NADPH:quinone reductase activity / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 2-(4-DIMETHYLAMINOPHENYL)DIAZENYLBENZOIC ACID / FMN-dependent NAD(P)H:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWang, C.-J. / Hagemeier, C. / Rahman, N. / Lowe, E.D. / Noble, M.E.M. / Coughtrie, M. / Sim, E. / Westwood, I.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular Cloning, Characterisation and Ligand- Bound Structure of an Azoreductase from Pseudomonas Aeruginosa
Authors: Wang, C.-J. / Hagemeier, C. / Rahman, N. / Lowe, E.D. / Noble, M.E.M. / Coughtrie, M. / Sim, E. / Westwood, I.M.
History
DepositionAug 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN-DEPENDENT NADH-AZOREDUCTASE 1
B: FMN-DEPENDENT NADH-AZOREDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4469
Polymers46,7192
Non-polymers1,7287
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-19.9 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.550, 82.550, 108.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2818, -0.7354, 0.6163), (-0.731, -0.5806, -0.3585), (0.6215, -0.3495, -0.7012)
Vector: 23.88, 41.56, -0.3387)

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Components

#1: Protein FMN-DEPENDENT NADH-AZOREDUCTASE 1 / FMN-DEPENDENT NADH-AZO COMPOUND OXIDOREDUCTASE 1 / AZO-DYE REDUCTASE 1


Mass: 23359.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FMN AND METHYL RED COMPLEX / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9I5F3, EC: 1.7.1.6
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MRE / 2-(4-DIMETHYLAMINOPHENYL)DIAZENYLBENZOIC ACID / METHYL RED


Mass: 269.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-((4-(DIMETHYLAMINO)PHENYL)DIAZENYL)BENZOIC ACID (MRE): METHYL RED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.4 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.6 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.18→34 Å / Num. obs: 20681 / % possible obs: 97.4 % / Observed criterion σ(I): 1.6 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1V4B AND 1T5B

1v4b

1t5b


Resolution: 2.18→34 Å / Stereochemistry target values: ML
Details: RESIDUES -2 - 1 ARE DISORDERED. RESIDUES 125 - 126 AND 187 - 192 OF CHAIN A ARE DISORDERED. RESIDUES 123 - 128 AND 187 - 198 OF CHAIN B ARE DISORDERED. REFMAC VERSION 5.3.0037 WAS USED FOR ...Details: RESIDUES -2 - 1 ARE DISORDERED. RESIDUES 125 - 126 AND 187 - 192 OF CHAIN A ARE DISORDERED. RESIDUES 123 - 128 AND 187 - 198 OF CHAIN B ARE DISORDERED. REFMAC VERSION 5.3.0037 WAS USED FOR REFINEMENT EXCEPT FOR THE FINAL REFINEMENT STEP, FOR WHICH PHENIX.REFINE WAS USED.
RfactorNum. reflection% reflection
Rfree0.242 2099 5.1 %
Rwork0.194 --
obs-38938 94.9 %
Refinement stepCycle: LAST / Resolution: 2.18→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 120 171 3339

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