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- PDB-7bx9: Purification, characterization and X-ray structure of YhdA-type a... -

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Basic information

Entry
Database: PDB / ID: 7bx9
TitlePurification, characterization and X-ray structure of YhdA-type azoreductase from Bacillus velezensis
ComponentsAzoreductaseAzobenzene reductase
KeywordsOXIDOREDUCTASE / Azo reductase / Azr / FMN / FLAVOPROTEIN
Function / homologyNADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Azoreductase
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsKhan, F. / Suguna, K.
CitationJournal: Proteins / Year: 2021
Title: Purification, characterization, and crystal structure of YhdA-type azoreductase from Bacillus velezensis.
Authors: Bafana, A. / Khan, F. / Suguna, K.
History
DepositionApr 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6448
Polymers18,6321
Non-polymers1,0127
Water3,963220
1
A: Azoreductase
hetero molecules

A: Azoreductase
hetero molecules

A: Azoreductase
hetero molecules

A: Azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57732
Polymers74,5304
Non-polymers4,04728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area17710 Å2
ΔGint-79 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.430, 102.470, 65.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-362-

HOH

31A-378-

HOH

41A-446-

HOH

51A-479-

HOH

61A-481-

HOH

71A-511-

HOH

81A-514-

HOH

91A-519-

HOH

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Components

#1: Protein Azoreductase / Azobenzene reductase


Mass: 18632.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: azr / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: B3VPZ9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 0.05 M Potassium phosphate monobasic, 20% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.38→36.71 Å / Num. obs: 51008 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 11.69 Å2 / CC1/2: 0.996 / Net I/σ(I): 10
Reflection shellResolution: 1.38→1.41 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2504 / CC1/2: 0.792

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSW

2gsw


Resolution: 1.38→30.97 Å / SU ML: 0.1158 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.2304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1515 2693 5.28 %
Rwork0.1306 48313 -
obs0.1317 51006 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.53 Å2
Refinement stepCycle: LAST / Resolution: 1.38→30.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 66 220 1583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471407
X-RAY DIFFRACTIONf_angle_d0.77561897
X-RAY DIFFRACTIONf_chiral_restr0.0711208
X-RAY DIFFRACTIONf_plane_restr0.0053236
X-RAY DIFFRACTIONf_dihedral_angle_d12.6764843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.26581530.20632504X-RAY DIFFRACTION99.96
1.41-1.430.16281390.16632515X-RAY DIFFRACTION100
1.43-1.460.18841250.14372539X-RAY DIFFRACTION100
1.46-1.50.15391620.13412478X-RAY DIFFRACTION99.96
1.5-1.530.15691350.12122515X-RAY DIFFRACTION100
1.53-1.570.14511400.11732544X-RAY DIFFRACTION100
1.57-1.610.12691390.1112502X-RAY DIFFRACTION100
1.61-1.660.16071420.11462537X-RAY DIFFRACTION99.89
1.66-1.710.13081370.11492527X-RAY DIFFRACTION99.81
1.71-1.770.14371590.11772479X-RAY DIFFRACTION99.89
1.77-1.840.16531350.12212539X-RAY DIFFRACTION99.78
1.84-1.930.15021520.1182536X-RAY DIFFRACTION99.93
1.93-2.030.1331390.11862545X-RAY DIFFRACTION100
2.03-2.160.1511400.11842531X-RAY DIFFRACTION100
2.16-2.320.13671420.1242556X-RAY DIFFRACTION100
2.32-2.560.15811210.12752579X-RAY DIFFRACTION100
2.56-2.930.1431490.13892570X-RAY DIFFRACTION100
2.93-3.690.15311440.1252606X-RAY DIFFRACTION100
3.69-30.970.15481400.15022711X-RAY DIFFRACTION99.65

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