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- PDB-4c0x: The crystal strucuture of PpAzoR in complex with anthraquinone-2-... -

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Basic information

Entry
Database: PDB / ID: 4c0x
TitleThe crystal strucuture of PpAzoR in complex with anthraquinone-2- sulfonate
ComponentsFMN-DEPENDENT NADH-AZOREDUCTASE 1
KeywordsOXIDOREDUCTASE / AZOREDUCTASE / NAD(P)H QUINONE OXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H, NAD(P) 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
9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid / FLAVIN MONONUCLEOTIDE / FMN-dependent NADH:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsGoncalves, A.M.D. / de Sanctis, D. / Bento, I.
CitationJournal: FEBS J. / Year: 2013
Title: The Crystal Structure of Pseudomonas Putida Azor: The Active Site Revisited.
Authors: Goncalves, A.M.D. / Mendes, S. / De Sanctis, D. / Martins, L.O. / Bento, I.
History
DepositionAug 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,7317
Polymers21,4141
Non-polymers1,3176
Water4,594255
1
A: FMN-DEPENDENT NADH-AZOREDUCTASE 1
hetero molecules

A: FMN-DEPENDENT NADH-AZOREDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,46314
Polymers42,8282
Non-polymers2,63512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7350 Å2
ΔGint-13.2 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.712, 94.947, 146.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-2039-

HOH

21A-2128-

HOH

31A-2169-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21414.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FMN-BINDING PROTEIN, COMPLEXED TO ANTHRAQUINONE-2-SULFONATE
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: MET94 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER
References: UniProt: Q88IY3, Oxidoreductases; Acting on other nitrogenous compounds as donors, NAD(P)H dehydrogenase (quinone)

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Non-polymers , 5 types, 261 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-AQN / 9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid


Mass: 288.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE GENOME OF PSEUDOMONAS PUTIDA STRAIN MET94 HAS NOT BEEN SEQUENCED TO DATE. THE HIGHEST HOMOLOGY ...THE GENOME OF PSEUDOMONAS PUTIDA STRAIN MET94 HAS NOT BEEN SEQUENCED TO DATE. THE HIGHEST HOMOLOGY IS WITH UNIPROT ENTRY Q88IY3, AZOR1 FROM P.PUTIDA KT2440, WITH ONLY ONE MUTATION ALA202(KT2440)TO VAL202(MET94)

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.0, 4% (V:V) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.5→47.5 Å / Num. obs: 40377 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 18.91 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C0W

4c0w


Resolution: 1.499→47.474 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 19.85 / Stereochemistry target values: ML / Details: RESIDUES 201-203 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.1925 2021 5 %
Rwork0.1686 --
obs0.1698 40373 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 1.499→47.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 77 255 1824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181667
X-RAY DIFFRACTIONf_angle_d1.8492277
X-RAY DIFFRACTIONf_dihedral_angle_d13.663596
X-RAY DIFFRACTIONf_chiral_restr0.123255
X-RAY DIFFRACTIONf_plane_restr0.009287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4994-1.5530.23862140.22993760X-RAY DIFFRACTION99
1.553-1.61520.23582110.20393844X-RAY DIFFRACTION100
1.6152-1.68870.23232010.19943788X-RAY DIFFRACTION99
1.6887-1.77780.20911880.18863793X-RAY DIFFRACTION99
1.7778-1.88910.20771840.17573758X-RAY DIFFRACTION98
1.8891-2.0350.19072040.17213783X-RAY DIFFRACTION98
2.035-2.23980.20332050.16863815X-RAY DIFFRACTION99
2.2398-2.56390.18012130.16733873X-RAY DIFFRACTION100
2.5639-3.23010.20281720.16933936X-RAY DIFFRACTION100
3.2301-47.49730.17472290.15364002X-RAY DIFFRACTION100

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