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- PDB-9j9j: Nitrophenol monooxygenase RsPNPA from Rhodococcus sp. 21391 -

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Basic information

Entry
Database: PDB / ID: 9j9j
TitleNitrophenol monooxygenase RsPNPA from Rhodococcus sp. 21391
Components4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


4-nitrocatechol 4-monooxygenase / 4-nitrophenol 2-monooxygenase / 4-nitrocatechol 4-monooxygenase activity / 4-nitrophenol 2-monooxygenase activity / oxidoreductase activity, acting on the CH-CH group of donors / catabolic process
Similarity search - Function
HpaB/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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component
Similarity search - Component
Biological speciesRhodococcus sp. 21391 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsYang, J. / Li, R. / Lin, S. / Long, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Microb Cell Fact / Year: 2025
Title: Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity.
Authors: Yang, J. / Lin, S. / Li, W. / Wang, X. / Li, R.
History
DepositionAug 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component
B: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component
C: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component


Theoretical massNumber of molelcules
Total (without water)182,6313
Polymers182,6313
Non-polymers00
Water2,198122
1
A: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component

A: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component

A: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component

A: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component


Theoretical massNumber of molelcules
Total (without water)243,5084
Polymers243,5084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area23960 Å2
ΔGint-196 kcal/mol
Surface area65040 Å2
MethodPISA
2
B: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component
C: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component

B: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component
C: 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component


Theoretical massNumber of molelcules
Total (without water)243,5084
Polymers243,5084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area22710 Å2
ΔGint-196 kcal/mol
Surface area64470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.561, 149.561, 322.141
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 4-nitrophenol 4-monooxygenase/4-nitrocatechol 2-monooxygenase, oxygenase component / 4-NP/4-NCA monooxygenase / PNP monooxygenase


Mass: 60876.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The sequence reference for Rhodococcus sp. 21391 (TAX ID 2683591), with the Genebank accession number WP_007295637, is not available in UniProt at the time of biocuration. Current sequence ...Details: The sequence reference for Rhodococcus sp. 21391 (TAX ID 2683591), with the Genebank accession number WP_007295637, is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID Q6F4M8.
Source: (gene. exp.) Rhodococcus sp. 21391 (bacteria) / Gene: npcA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6F4M8, 4-nitrocatechol 4-monooxygenase, 4-nitrophenol 2-monooxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.056 M NaH2PO4, 1.344 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.32 Å / Num. obs: 71504 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 1.02 / Net I/σ(I): 21.2
Reflection shellResolution: 2.4→2.45 Å / % possible obs: 99.1 % / Redundancy: 13.7 % / Rmerge(I) obs: 1.141 / Num. measured all: 62127 / Num. unique obs: 4527 / CC1/2: 0.923 / Rpim(I) all: 0.317 / Rrim(I) all: 1.185 / Χ2: 1 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.218 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.421 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28188 3620 5.1 %RANDOM
Rwork0.22727 ---
obs0.23006 67885 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.615 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å2-0 Å2
2--0.79 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 2.4→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11719 0 0 122 11841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01212023
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611038
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.81416369
X-RAY DIFFRACTIONr_angle_other_deg0.561.76125297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6751465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.28596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.993101878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.21765
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022976
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4845.5365878
X-RAY DIFFRACTIONr_mcbond_other4.4775.5375878
X-RAY DIFFRACTIONr_mcangle_it6.2199.9467337
X-RAY DIFFRACTIONr_mcangle_other6.229.9467338
X-RAY DIFFRACTIONr_scbond_it4.9315.9576145
X-RAY DIFFRACTIONr_scbond_other4.9315.9576146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.19510.7689033
X-RAY DIFFRACTIONr_long_range_B_refined9.00652.3413499
X-RAY DIFFRACTIONr_long_range_B_other9.01252.3613477
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å
RfactorNum. reflection% reflection
Rfree0.356 248 -
Rwork0.317 4934 -
obs--99.04 %

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