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- PDB-7dbw: PnpA1, the oxygenase component of a two-component para-nitropheno... -

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Basic information

Entry
Database: PDB / ID: 7dbw
TitlePnpA1, the oxygenase component of a two-component para-nitrophenol hydroxylase from Rhodococcus imtechensis RKJ300
Components4-hydroxyphenylacetate 3-hydroxylase
KeywordsOXIDOREDUCTASE / para-nitrophenol / flavin-dependent two-component monooyxgenase / hydroxylase / biodegradation
Function / homologyHpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / oxidoreductase activity, acting on the CH-CH group of donors / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / 4-hydroxyphenylacetate 3-hydroxylase
Function and homology information
Biological speciesRhodococcus imtechensis RKJ300 = JCM 13270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGuo, Y. / Zheng, J.T. / Zhou, N.Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0901200 China
National Natural Science Foundation of China (NSFC)31670107 China
National Natural Science Foundation of China (NSFC)31770068 China
CitationJournal: Appl.Environ.Microbiol. / Year: 2021
Title: Single-Component and Two-Component para -Nitrophenol Monooxygenases: Structural Basis for Their Catalytic Difference.
Authors: Guo, Y. / Li, D.F. / Zheng, J. / Xu, Y. / Zhou, N.Y.
History
DepositionOct 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
C: 4-hydroxyphenylacetate 3-hydroxylase
A: 4-hydroxyphenylacetate 3-hydroxylase
B: 4-hydroxyphenylacetate 3-hydroxylase


Theoretical massNumber of molelcules
Total (without water)179,4173
Polymers179,4173
Non-polymers00
Water1,33374
1
C: 4-hydroxyphenylacetate 3-hydroxylase

C: 4-hydroxyphenylacetate 3-hydroxylase

C: 4-hydroxyphenylacetate 3-hydroxylase

C: 4-hydroxyphenylacetate 3-hydroxylase


Theoretical massNumber of molelcules
Total (without water)239,2234
Polymers239,2234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445-y-1,-x-1,-z1
crystal symmetry operation10_445-x-1,-y-1,z1
crystal symmetry operation15_555y,x,-z1
Buried area25180 Å2
ΔGint-189 kcal/mol
Surface area65960 Å2
MethodPISA
2
A: 4-hydroxyphenylacetate 3-hydroxylase
B: 4-hydroxyphenylacetate 3-hydroxylase

A: 4-hydroxyphenylacetate 3-hydroxylase
B: 4-hydroxyphenylacetate 3-hydroxylase


Theoretical massNumber of molelcules
Total (without water)239,2234
Polymers239,2234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area25160 Å2
ΔGint-190 kcal/mol
Surface area65250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.007, 150.007, 321.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein 4-hydroxyphenylacetate 3-hydroxylase


Mass: 59805.770 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus imtechensis RKJ300 = JCM 13270 (bacteria)
Gene: W59_00989 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I0WZP1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1 M Tris (pH 7.25), 1.5 M (NH4)2SO4 and 4% v/v glycerol

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 63441 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Χ2: 0.381 / Net I/σ(I): 13.14
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3097 / CC1/2: 0.976 / CC star: 0.994 / Rpim(I) all: 0.18 / Rrim(I) all: 0.642 / Χ2: 0.415 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMACphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G5E

4g5e


Resolution: 2.5→22.78 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 40.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2913 3212 5.1 %
Rwork0.2418 59779 -
obs0.2444 62991 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.97 Å2 / Biso mean: 39.8107 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 2.5→22.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11895 0 0 74 11969
Biso mean---28.89 -
Num. residues----1494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.540.31581490.29462493264298
2.54-2.580.38551300.283525792709100
2.58-2.620.32271430.283525562699100
2.62-2.660.34831400.270825842724100
2.66-2.710.32351340.283725822716100
2.71-2.770.35321350.28525702705100
2.77-2.820.31121290.281825952724100
2.82-2.880.35011430.262225892732100
2.88-2.950.2961490.26525822731100
2.95-3.020.28321460.26825682714100
3.02-3.10.33531300.2642586271699
3.1-3.20.33921460.25722575272199
3.2-3.30.28521370.251725842721100
3.3-3.420.31861450.247325952740100
3.42-3.550.32551210.2326262747100
3.55-3.710.27171480.223125972745100
3.71-3.910.2591380.214125952733100
3.91-4.150.24521370.204626402777100
4.15-4.470.17851320.192426312763100
4.47-4.920.23131260.203526482774100
4.92-5.620.32561530.22452641279499
5.62-7.040.35961450.25952664280999
7.04-22.780.27911560.25492699285596

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