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- PDB-3bw4: Crystal structures and site-directed mutagenesis study of nitroal... -

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Basic information

Entry
Database: PDB / ID: 3bw4
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 / Propionate 3-nitronate monooxygenase
Similarity search - Component
Biological speciesStreptomyces ansochromogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, Y.H. / Gao, Z.Q. / Hou, H.F.
CitationJournal: To be Published
Title: Crystal structures and site-directed mutagenesis study of nitroalkane oxidase from Streptomyces ansochromogenes
Authors: Li, Y.H. / Gao, Z.Q. / Hou, H.F. / 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 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-nitropropane dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0963
Polymers38,5211
Non-polymers5752
Water2,450136
1
A: 2-nitropropane dioxygenase
hetero molecules

A: 2-nitropropane dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1926
Polymers77,0432
Non-polymers1,1494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x,-y+1/2,-z-3/41
Buried area5450 Å2
ΔGint-43.9 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.319, 113.319, 115.334
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: 38521.328 Da / Num. of mol.: 1 / Mutation: W320Y
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 / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 48.81 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 25547 / Num. obs: 22020 / % possible obs: 86.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.8 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.53 / Num. unique all: 2524 / % possible all: 99.6

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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→30 Å / σ(F): 1 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.216 910 4.7 %RANDOM
Rwork0.185 ---
obs0.185 18676 96.4 %-
all-19378 --
Displacement parametersBiso mean: 29.12 Å2
Baniso -1Baniso -2Baniso -3
1--5.012 Å20 Å20 Å2
2---5.012 Å20 Å2
3---10.023 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 39 136 2705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d21.92
X-RAY DIFFRACTIONc_improper_angle_d1.19
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3FMN.param
X-RAY DIFFRACTION4MPD.param

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