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- PDB-3bw3: Crystal structures and site-directed mutagenesis study of nitroal... -

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Basic information

Entry
Database: PDB / ID: 3bw3
TitleCrystal structures and site-directed mutagenesis study of nitroalkane oxidase from Streptomyces ansochromogenes
Components2-nitropropane dioxygenase
KeywordsOXIDOREDUCTASE / TIM barrel / Dioxygenase
Function / homology
Function and homology information


nitronate monooxygenase activity / dioxygenase activity / response to toxic substance / nucleotide binding
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / nitroethane / Probable nitronate monooxygenase
Similarity search - Component
Biological speciesStreptomyces ansochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, Y.H. / Gao, Z.Q. / Hou, H.F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure and site-directed mutagenesis of a nitroalkane oxidase from Streptomyces ansochromogenes
Authors: Li, Y.H. / Gao, Z.Q. / Hou, H.F. / Li, L. / Zhang, J.H. / Yang, H.H. / Dong, Y.H. / Tan, H.R.
History
DepositionJan 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 2-nitropropane dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2895
Polymers38,5211
Non-polymers7684
Water2,864159
1
A: 2-nitropropane dioxygenase
hetero molecules

A: 2-nitropropane dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57810
Polymers77,0432
Non-polymers1,5368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x,-y+3/2,-z-3/41
Buried area5940 Å2
ΔGint-60.3 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.465, 113.465, 115.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein 2-nitropropane dioxygenase


Mass: 38521.305 Da / Num. of mol.: 1 / Mutation: H179D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ansochromogenes (bacteria)
Strain: 7100 / Gene: 2-npdl / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9FDD4, nitroalkane oxidase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NIE / nitroethane


Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M ammonium dihydrogen phosphate, 0.1M Tris-Cl, 50% MPD, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 34891 / Num. obs: 30092 / % possible obs: 86.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.5 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.489 / Num. unique all: 3436 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BW2

3bw2


Resolution: 2.2→10 Å / σ(F): 1 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.207 888 4.6 %RANDOM
Rwork0.185 ---
obs0.185 18777 97.7 %-
all-19215 --
Displacement parametersBiso mean: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.128 Å20 Å20 Å2
2---1.128 Å20 Å2
3---2.255 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 52 159 2735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.18
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3FMN.param
X-RAY DIFFRACTION4MPD.param
X-RAY DIFFRACTION5NIE.param

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