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- PDB-3p0r: Crystal structure of azoreductase from Bacillus anthracis str. Sterne -

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Basic information

Entry
Database: PDB / ID: 3p0r
TitleCrystal structure of azoreductase from Bacillus anthracis str. Sterne
ComponentsAzoreductaseAzobenzene reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Azoreductase
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor / oxidoreductase activity, acting on other nitrogenous compounds as donors / 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
DI(HYDROXYETHYL)ETHER / : / FMN-dependent NADH-azoreductase 4
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.799 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of azoreductase from Bacillus anthracis str. Sterne
Authors: Filippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7475
Polymers23,4181
Non-polymers3304
Water3,099172
1
A: Azoreductase
hetero molecules

A: Azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,49510
Polymers46,8352
Non-polymers6598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4800 Å2
ΔGint-76 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.391, 101.262, 63.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Azoreductase / Azobenzene reductase


Mass: 23417.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAA_5688 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: C3P2H0, UniProt: Q81JP2*PLUS

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2M NH4 Sulfate, 1% PEG2KMME, 0.2M MgCl2, 0.1M Bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 16, 2010 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.799→30 Å / Num. all: 21314 / Num. obs: 21314 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 32.5
Reflection shellResolution: 1.799→1.83 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
CCP4model building
MrBUMPphasing
REFMAC5.5.0109refinement
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.799→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.475 / SU ML: 0.078 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23377 1086 5.1 %RANDOM
Rwork0.18818 ---
obs0.19038 20038 99.07 %-
all-20038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.77 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.799→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 19 172 1803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221662
X-RAY DIFFRACTIONr_bond_other_d0.0010.021103
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9752248
X-RAY DIFFRACTIONr_angle_other_deg0.89932711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8055207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32225.55672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72915277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.769153
X-RAY DIFFRACTIONr_chiral_restr0.090.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211841
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02321
X-RAY DIFFRACTIONr_mcbond_it0.8251.51033
X-RAY DIFFRACTIONr_mcbond_other0.2651.5422
X-RAY DIFFRACTIONr_mcangle_it1.43821656
X-RAY DIFFRACTIONr_scbond_it2.5763629
X-RAY DIFFRACTIONr_scangle_it4.1414.5592
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 83 -
Rwork0.193 1445 -
obs--99.16 %
Refinement TLS params.Method: refined / Origin x: 19.377 Å / Origin y: 43.0312 Å / Origin z: 41.1579 Å
111213212223313233
T0.0288 Å2-0.0087 Å2-0.0082 Å2-0.041 Å20.0106 Å2--0.0123 Å2
L0.6103 °2-0.153 °2-0.1611 °2-1.3849 °20.0573 °2--0.6356 °2
S-0.0103 Å °-0.0614 Å °-0.0073 Å °0.0836 Å °-0.0279 Å °-0.0856 Å °0.0671 Å °-0.0037 Å °0.0382 Å °

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