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- PDB-3w7a: Crystal Structure of azoreductase AzrC fin complex with sulfone-m... -

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Basic information

Entry
Database: PDB / ID: 3w7a
TitleCrystal Structure of azoreductase AzrC fin complex with sulfone-modified azo dye Acid Red 88
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / azoreductase / azo bond cleavage / FMN-binding / azoreductase-azoreductase substrate complex
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 / metal ion binding
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 / : / Chem-RE8 / FMN dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesBacillus (Bacillus rRNA group 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYu, J. / Ogata, D. / 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 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
C: FMN-dependent NADH-azoreductase
D: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,41919
Polymers91,8034
Non-polymers3,61615
Water4,179232
1
A: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6899
Polymers45,9022
Non-polymers1,7887
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-39 kcal/mol
Surface area18490 Å2
MethodPISA
2
C: FMN-dependent NADH-azoreductase
D: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,72910
Polymers45,9022
Non-polymers1,8288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-46 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.982, 56.618, 105.518
Angle α, β, γ (deg.)90.000, 115.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 22950.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Strain: B29 / Gene: azrC, azoR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C0STY1, Oxidoreductases; Acting on other nitrogenous compounds as donors

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Non-polymers , 5 types, 247 molecules

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


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-RE8 / 4-[(E)-(2-hydroxynaphthalen-1-yl)diazenyl]naphthalene-1-sulfonic acid / Acid red 88


Mass: 378.401 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H14N2O4S
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.81 Å3/Da / Density % sol: 56.29 % / Mosaicity: 0.723 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 600, pH 6.5, 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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 59046 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.171 / Χ2: 3.128 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1840.49756281.735194.8
2.18-2.264.30.42656951.627196.9
2.26-2.374.60.39858641.422198.8
2.37-2.4950.35658761.633199.3
2.49-2.655.30.31459311.725199.8
2.65-2.855.60.26159892.051100
2.85-3.145.70.19559331.621100
3.14-3.595.70.14359731.7081100
3.59-4.525.70.11160092.231100
4.52-505.60.081614813.615199.8

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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
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W77

3w77


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.46 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 4149 7.1 %RANDOM
Rwork0.1986 ---
obs0.2015 58641 97.19 %-
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: 71.37 Å2 / Biso mean: 25.071 Å2 / Biso min: 7.25 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å2-1.04 Å2
2--2.79 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 239 232 6911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026836
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9779320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36425.513312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.354151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0381516
X-RAY DIFFRACTIONr_chiral_restr0.1210.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215292
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 252 -
Rwork0.224 3134 -
all-3386 -
obs--79.78 %
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)
10.46250.0897-0.24360.2428-0.20790.55950.01150.0637-0.00680.0331-0.01420.0014-0.0404-0.00450.00270.0448-0.00790.00250.01420.00470.03338.0011-28.367230.7252
20.73330.2316-0.07890.1810.03510.22410.00980.1157-0.00470.0003-0.0215-0.0319-0.0212-0.03820.01170.0374-0.01240.00950.05540.01140.017155.8656-27.836813.8591
30.32230.11360.14620.28890.30250.63970.01510.04660.0230.0248-0.015-0.01490.01590.014-0.00010.0437-0.0032-0.00860.0159-0.00290.039312.55110.746529.9343
40.78530.1570.17360.3327-0.06180.3610.01630.1021-0.00180.0116-0.0309-0.00330.00660.01790.01470.0252-0.012700.0304-0.00070.0007-5.355-0.085913.175
512.3988-4.1134-1.16791.51680.71420.8565-0.16260.0072-0.3840.1096-0.03780.19120.2144-0.09080.20030.1779-0.02540.05390.0205-0.01880.091846.7474-42.547925.6865
68.5821-5.9317-0.78574.7636-0.81612.85550.2493-0.1068-0.0730.1405-0.00560.1652-0.69720.1321-0.24370.1791-0.04340.02950.04630.02540.088450.1651-13.657122.0608
715.23370.10594.16761.4115-0.85061.6893-0.2639-0.1180.1885-0.02230.057-0.2196-0.0639-0.05530.20690.07420.0044-0.03240.05140.02110.10323.804914.815824.6997
87.82611.53872.93536.30682.96952.05520.26310.1386-0.25360.2661-0.0412-0.27730.20520.0391-0.22180.15810.0093-0.03540.0307-0.01120.07430.7142-14.211321.2889
90.0367-0.77220.290117.4658-1.862226.23720.136-0.0287-0.0240.34990.9950.6232-0.7998-0.3768-1.13110.14940.1043-0.01380.18190.16560.41951.266117.464421.9682
1043.738624.988116.916517.18275.496112.73660.79310.0495-0.4101-0.2626-0.20680.12281.190.4853-0.58630.29830.098-0.02590.1724-0.09220.258949.5453-45.632523.6174
1119.9237-6.5186.642530.7844-1.09182.259-0.9649-0.1381-1.29080.60231.33260.2517-0.29930.0302-0.36770.49580.17280.06870.34670.18020.24233.3997-17.095623.5476
1233.6199-10.63587.759845.2621-11.87423.9087-0.7427-0.57082.03960.30190.35270.1684-0.2056-0.15020.390.45920.12780.12230.1229-0.06750.282247.7674-10.653824.6724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 211
2X-RAY DIFFRACTION2B2 - 211
3X-RAY DIFFRACTION3C2 - 211
4X-RAY DIFFRACTION4D2 - 211
5X-RAY DIFFRACTION5A301
6X-RAY DIFFRACTION6B301
7X-RAY DIFFRACTION7C301
8X-RAY DIFFRACTION8D301
9X-RAY DIFFRACTION9C302
10X-RAY DIFFRACTION10A302
11X-RAY DIFFRACTION11C303
12X-RAY DIFFRACTION12A303

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