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- PDB-1nni: Azobenzene Reductase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1nni
TitleAzobenzene Reductase from Bacillus subtilis
Componentshypothetical protein yhdaHypothesis
KeywordsOXIDOREDUCTASE / azobenzene reductase / azoreductase / structural genomics / flavoproteins / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / FMN binding / oxidoreductase activity / identical protein binding / cytosol
Similarity search - Function
NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-dependent NADPH-azoreductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsCuff, M.E. / Kim, Y. / Maj, L. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2003
Title: Azobenzene Reductase from Bacillus subtilis
Authors: Cuff, M.E. / Kim, Y. / Maj, L. / Collart, F. / Joachimiak, A.
History
DepositionJan 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: hypothetical protein yhda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6642
Polymers19,2071
Non-polymers4561
Water2,486138
1
1: hypothetical protein yhda
hetero molecules

1: hypothetical protein yhda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3274
Polymers38,4142
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/31
Unit cell
Length a, b, c (Å)112.720, 112.720, 90.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Cell settinghexagonal
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
111-279-

HOH

Detailslikely a dimer related by the crystallographic two fold axis: 1-y, 1-x, 3/2-z

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Components

#1: Protein hypothetical protein yhda / Hypothesis / E.C.1.7.1.6 / azobenzene reductase / Azoreductase


Mass: 19207.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: apc1167 / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yhda / Production host: Escherichia coli (E. coli) / References: UniProt: O07529, EC: 1.7.1.6
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.99 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: trisodium citrate, sodium HEPES, sucrose, pH 7.5-8.5, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97940, 0.97926, 0.95372
DetectorType: SBC-2 / Detector: CCD / Date: Aug 31, 2002
RadiationMonochromator: sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979261
30.953721
ReflectionResolution: 2.5→50 Å / Num. all: 22141 / Num. obs: 19743 / % possible obs: 89.2 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38.1 Å2 / Limit h max: 40 / Limit h min: 0 / Limit k max: 23 / Limit k min: 0 / Limit l max: 36 / Limit l min: -36 / Observed criterion F max: 2577691.04 / Observed criterion F min: 3.489

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→48.81 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1593 9.2 %random
Rwork0.221 ---
all0.238 22142 --
obs0.223 17370 78.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 50.1134 Å2 / ksol: 0.330555 e/Å3
Displacement parametersBiso max: 100.88 Å2 / Biso mean: 52.95 Å2 / Biso min: 29.36 Å2
Baniso -1Baniso -2Baniso -3
1--10.64 Å2-0.89 Å20 Å2
2---10.64 Å20 Å2
3---21.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.47 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 31 138 1478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_torsion_deg22
X-RAY DIFFRACTIONx_torsion_impr_deg0.88
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.35610590.32910600.0352753116542.3
2.61-2.750.3281197.60.29914480.032766156756.6
2.75-2.920.32717990.28918190.0242774199872
2.92-3.150.2842309.90.27121020.0192772233284.1
3.15-3.470.23827911.10.23622270.0142780250690.1
3.47-3.970.24320780.19523870.0172765259493.8
3.97-50.177265100.17123860.0112774265195.6
5-48.810.2472098.20.22623480.0172779255792

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