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- PDB-1v4b: The crystal structure of AzoR (Azo Reductase) from Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 1v4b
TitleThe crystal structure of AzoR (Azo Reductase) from Escherichia coli: Oxidized form
ComponentsNADH-azoreductase, FMN-dependent
KeywordsOXIDOREDUCTASE / Azo Reductase
Function / homology
Function and homology information


azobenzene reductase activity / 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 / response to oxidative stress / electron transfer activity / protein homodimerization activity / cytosol
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 / ISOPROPYL ALCOHOL / FMN-dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsIto, K. / Tanokura, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Three-dimensional structure of AzoR from Escherichia coli. An oxidereductase conserved in microorganisms
Authors: Ito, K. / Nakanishi, M. / Lee, W.C. / Sasaki, H. / Zenno, S. / Saigo, K. / Kitade, Y. / Tanokura, M.
History
DepositionNov 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: NADH-azoreductase, FMN-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1264
Polymers21,5471
Non-polymers5793
Water2,522140
1
A: NADH-azoreductase, FMN-dependent
hetero molecules

A: NADH-azoreductase, FMN-dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2528
Polymers43,0952
Non-polymers1,1576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)92.185, 92.185, 51.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

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Components

#1: Protein NADH-azoreductase, FMN-dependent / Azo Reductase / AzoR


Mass: 21547.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41407, EC: 1.7.1.6
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.06 %

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Data collection

Diffraction
IDCrystal-ID
11
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONSPring-8 BL41XU21
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 23, 2000
ADSC QUANTUM 42CCDJun 25, 2000
MARRESEARCH3CCDMar 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→64.55 Å / Num. obs: 20095

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→21.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.725 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23426 1091 5.1 %RANDOM
Rwork0.19215 ---
obs0.19424 20095 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 35 144 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221559
X-RAY DIFFRACTIONr_bond_other_d0.0210.021437
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9932120
X-RAY DIFFRACTIONr_angle_other_deg1.06233342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64615269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021707
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02289
X-RAY DIFFRACTIONr_nbd_refined0.2020.2305
X-RAY DIFFRACTIONr_nbd_other0.2620.21602
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.2892
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1570.55
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0670.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2551.5979
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96821573
X-RAY DIFFRACTIONr_scbond_it3.0213580
X-RAY DIFFRACTIONr_scangle_it4.5564.5547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 83
Rwork0.241 1401

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