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- PDB-3w78: Crystal Structure of azoreductase AzrC in complex with NAD(P)-inh... -

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Basic information

Entry
Database: PDB / ID: 3w78
TitleCrystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor Cibacron Blue
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE/ OXIDOREDUCTASE INHIBITOR / azoreductase / azo bond cleavage / FMN-binding / OXIDOREDUCTASE- OXIDOREDUCTASE INHIBITOR 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, NAD(P) 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
CIBACRON BLUE / FLAVIN MONONUCLEOTIDE / FMN dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesBacillus (Bacillus rRNA group 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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 / Item: _software.name
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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
D: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
C: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,72512
Polymers91,8034
Non-polymers4,9228
Water37821
1
A: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3636
Polymers45,9022
Non-polymers2,4614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-54 kcal/mol
Surface area18150 Å2
MethodPISA
2
D: FMN-dependent NADH-azoreductase
hetero molecules

D: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3636
Polymers45,9022
Non-polymers2,4614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6620 Å2
ΔGint-51 kcal/mol
Surface area18200 Å2
MethodPISA
3
C: FMN-dependent NADH-azoreductase
hetero molecules

C: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3636
Polymers45,9022
Non-polymers2,4614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6640 Å2
ΔGint-52 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.370, 146.370, 116.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22B
13A
23C
14D
24B
15D
25C
16B
26C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 2 - 211 / Label seq-ID: 2 - 211

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21DB
12AA
22BC
13AA
23CD
14DB
24BC
15DB
25CD
16BC
26CD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-CBD / CIBACRON BLUE


Mass: 774.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H20ClN7O11S3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 600, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 43062 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 53.468 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 23.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.62-2.780.9040.6363.3454398691167310.67997.4
2.78-2.970.9580.415.1754888653265250.43699.9
2.97-3.210.9840.2199.2950863605460480.23399.9
3.21-3.520.9950.11817.6246879561056080.126100
3.52-3.930.9980.06829.6342035508050620.07399.6
3.93-4.530.9990.04442.636937450744870.04799.6
4.53-5.540.9990.03749.3831416385238400.03999.7
5.54-7.780.9990.03153.9724355302630250.033100
7.78-47.9110.9990.02469.2412554178417360.02597.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W7A

3w7a


Resolution: 2.62→50 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.886 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.183 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.496 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 3079 7.2 %RANDOM
Rwork0.2527 ---
obs0.255 43062 99.25 %-
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: 114.81 Å2 / Biso mean: 69.515 Å2 / Biso min: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.37 Å20 Å2
2--0.73 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.62→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 328 21 6789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.026940
X-RAY DIFFRACTIONr_angle_refined_deg1.0271.9969492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7825836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68925.513312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7581516
X-RAY DIFFRACTIONr_chiral_restr0.0690.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215360
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2350.1
12D2350.1
21A2450.04
22B2450.04
31A2120.16
32C2120.16
41D2460.07
42B2460.07
51D2180.15
52C2180.15
61B2160.15
62C2160.15
LS refinement shellResolution: 2.623→2.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 193 -
Rwork0.326 2625 -
all-2818 -
obs--94.03 %
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)
11.0370.18970.25681.3826-0.57722.1472-0.10360.1303-0.00260.08520.085-0.01120.0350.00650.01860.166-0.01580.04430.08450.01260.0579-75.108131.77341.0062
21.1323-0.29170.59763.2762-1.55092.8763-0.00660.11690.213-0.1398-0.3648-0.9346-0.12340.29610.37140.0568-0.00090.05430.13520.08530.3284-50.209910.218512.6631
31.22210.21080.64453.3382-0.65941.9512-0.1195-0.06260.00910.12020.57620.7989-0.0081-0.6458-0.45660.1554-0.04180.07580.39780.2360.3045-99.464431.51920.5045
42.9069-0.21521.29595.3853-1.50321.5745-0.18-0.1199-0.2052-0.32451.39141.8614-0.1459-0.5382-1.21150.0765-0.08450.04121.01410.91881.3702-125.05578.496111.3906
55.23491.6347-0.3930.792-0.12810.030.47030.0461.2860.7566-0.23020.3324-0.05090.0207-0.24021.62610.34010.6811.26430.73861.3803-115.190723.902326.4605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 211
2X-RAY DIFFRACTION2D2 - 211
3X-RAY DIFFRACTION3B2 - 211
4X-RAY DIFFRACTION4C2 - 185
5X-RAY DIFFRACTION5C186 - 211

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