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- PDB-2z9d: The crystal structure of AzoR (azoreductase) from Escherichia col... -

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Basic information

Entry
Database: PDB / ID: 2z9d
TitleThe crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / azoreductase / Flavoprotein / FMN / NAD
Function / homology
Function and homology information


azobenzene reductase activity / FMN-dependent NADH-azoreductase / 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 / 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 / FMN-dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIto, K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Expansion of Substrate Specificity and Catalytic Mechanism of Azoreductase by X-ray Crystallography and Site-directed Mutagenesis
Authors: Ito, K. / Nakanishi, M. / Lee, W.C. / Zhi, Y. / Sasaki, H. / Zenno, S. / Saigo, K. / Kitade, Y. / Tanokura, M.
History
DepositionSep 18, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0084
Polymers43,0952
Non-polymers9132
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-29.3 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.065, 89.892, 101.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FMN-dependent NADH-azoreductase / FMN-dependent NADH-azo compound oxidoreductase / Azo-dye reductase


Mass: 21547.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: azoR / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P41407, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.95 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→67.42 Å / Num. obs: 29939

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1V4B

1v4b


Resolution: 2.1→41.17 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.789 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21395 1519 5.1 %RANDOM
Rwork0.16979 ---
obs0.17202 28382 99.03 %-
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: 23.502 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20 Å2
2---1.51 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 62 164 3266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223164
X-RAY DIFFRACTIONr_bond_other_d0.0010.022066
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9984314
X-RAY DIFFRACTIONr_angle_other_deg0.91835080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73924.762126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64115510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5541514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_nbd_refined0.2060.2530
X-RAY DIFFRACTIONr_nbd_other0.1910.22036
X-RAY DIFFRACTIONr_nbtor_refined0.180.21565
X-RAY DIFFRACTIONr_nbtor_other0.0860.21513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1821.52565
X-RAY DIFFRACTIONr_mcbond_other0.2261.5806
X-RAY DIFFRACTIONr_mcangle_it1.38823210
X-RAY DIFFRACTIONr_scbond_it2.56531427
X-RAY DIFFRACTIONr_scangle_it3.4314.51104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 123 -
Rwork0.182 2025 -
obs--99.86 %

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