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- PDB-3w77: Crystal Structure of azoreductase AzrA -

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Basic information

Entry
Database: PDB / ID: 3w77
TitleCrystal Structure of azoreductase AzrA
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / azoreductase / azo bond cleavage / FMN-binding
Function / homology
Function and homology information


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 / 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
Similarity search - Component
Biological speciesBacillus (Bacillus rRNA group 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsOgata, D. / Yu, J. / Ooi, T. / Yao, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of AzrA and of AzrC complexed with substrate or inhibitor: insight into substrate specificity and catalytic mechanism.
Authors: Yu, J. / Ogata, D. / Gai, Z. / Taguchi, S. / Tanaka, I. / Ooi, T. / Yao, M.
History
DepositionFeb 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 20, 2024Group: 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: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4934
Polymers45,5802
Non-polymers9132
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-30 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.323, 69.589, 105.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22790.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Strain: B29 / Gene: azrA, azoR / Production host: Escherichia coli (E. coli)
References: UniProt: Q0WXX2, Oxidoreductases; Acting on other nitrogenous compounds as donors
#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.: 307 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: PEG 600, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979121 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979121 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 50324 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.078 / Χ2: 2.061 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.66-1.726.10.47649160.691199
1.72-1.796.60.37449710.707199.7
1.79-1.876.80.27249610.738199.9
1.87-1.976.80.17949760.823199.9
1.97-2.096.90.12549990.9861100
2.09-2.2570.09449981.1721100
2.25-2.487.10.08250401.582199.9
2.48-2.847.10.0950473.2261100
2.84-3.586.90.06751053.9321100
3.58-506.80.0553116.157199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→44.24 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.457 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 3549 7.1 %RANDOM
Rwork0.1783 ---
obs0.1806 50262 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 45.67 Å2 / Biso mean: 20.45 Å2 / Biso min: 6.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.88 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.66→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 62 307 3565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023332
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9884528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0415412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27525.556144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6915540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.222156
X-RAY DIFFRACTIONr_chiral_restr0.1020.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212516
LS refinement shellResolution: 1.661→1.704 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 247 -
Rwork0.212 3137 -
all-3384 -
obs--97.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2483-0.0390.01070.629-0.28351.18980.04430.0380.0275-0.0412-0.0507-0.04650.0570.16110.00640.01130.01440.0070.02740.00370.024636.663135.697646.6907
20.23770.00440.16170.45960.35941.23520.0302-0.05870.0370.0293-0.05460.05260.0432-0.14060.02440.0131-0.01290.01260.0254-0.01380.028516.140936.452459.7552
30.3604-0.00760.04550.38120.03480.86280.0211-0.00140.02070.026-0.01860.01160.04460.0176-0.00250.036-0.00070.00170.0014-0.00130.056425.040434.319652.4159
49.0944-8.8088-4.83213.55861.64634.50320.13990.2156-0.1488-0.2648-0.07460.3247-0.098-0.1722-0.06530.1191-0.0212-0.01590.0313-0.0060.067921.782838.039939.625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 208
2X-RAY DIFFRACTION2B3 - 208
3X-RAY DIFFRACTION3A401 - 544
4X-RAY DIFFRACTION3B401 - 563
5X-RAY DIFFRACTION4A301

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