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- PDB-4c0w: The crystal strucuture of native PpAzoR -

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Basic information

Entry
Database: PDB / ID: 4c0w
TitleThe crystal strucuture of native PpAzoR
ComponentsFMN-DEPENDENT NADH-AZOREDUCTASE 1
KeywordsOXIDOREDUCTASE
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 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 / FMN-dependent NADH:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.6 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 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)22,9644
Polymers21,4141
Non-polymers1,5503
Water5,441302
1
A: FMN-DEPENDENT NADH-AZOREDUCTASE 1
hetero molecules

A: FMN-DEPENDENT NADH-AZOREDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9288
Polymers42,8282
Non-polymers3,0996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6170 Å2
ΔGint-51.9 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.299, 95.743, 146.539
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-2055-

HOH

21A-2080-

HOH

31A-2154-

HOH

41A-2198-

HOH

51A-2275-

HOH

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Components

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


Mass: 21414.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: MET94 / Plasmid: PET-21A / 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)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7
Details: 4% PEG 400, 2M AMMONIUM SULPHATE, 0.1M HEPES PH 7.0 AT 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.6→53.7 Å / Num. obs: 33249 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 17.65 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.9

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.6→26.13 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 16.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 1683 5.1 %
Rwork0.1528 --
obs0.1541 33239 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 57 302 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011673
X-RAY DIFFRACTIONf_angle_d1.282288
X-RAY DIFFRACTIONf_dihedral_angle_d13.212621
X-RAY DIFFRACTIONf_chiral_restr0.08261
X-RAY DIFFRACTIONf_plane_restr0.006292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64710.22211570.19552608X-RAY DIFFRACTION100
1.6471-1.70020.21541180.19252652X-RAY DIFFRACTION100
1.7002-1.7610.25161410.1912638X-RAY DIFFRACTION100
1.761-1.83150.2121470.1792618X-RAY DIFFRACTION100
1.8315-1.91480.18231280.1762650X-RAY DIFFRACTION100
1.9148-2.01570.21391430.16772634X-RAY DIFFRACTION100
2.0157-2.1420.19011400.1452666X-RAY DIFFRACTION100
2.142-2.30730.1671530.1332613X-RAY DIFFRACTION100
2.3073-2.53930.15291460.1342623X-RAY DIFFRACTION100
2.5393-2.90630.1421390.13992673X-RAY DIFFRACTION99
2.9063-3.660.16271370.14392645X-RAY DIFFRACTION98
3.66-26.13340.19221340.15612536X-RAY DIFFRACTION91

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