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- PDB-6ain: Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseu... -

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Basic information

Entry
Database: PDB / ID: 6ain
TitleCrystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseudomonas putida DLL-E4
ComponentsPnpA
KeywordsFLAVOPROTEIN / p-Nitrophenol 4-monooxygenase
Function / homology3-(3-hydroxyphenyl)propionate hydroxylase activity / : / 3-(3-hydroxy)phenylpropionate catabolic process / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / PnpA
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsChen, Q.Z. / Huang, Y. / Duan, Y.J. / Li, Z.K. / Liu, W.D. / Cui, Z.L.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseudomonas putida DLL-E4: The key enzyme involved in p-nitrophenol degradation.
Authors: Chen, Q.Z. / Huang, Y. / Duan, Y.J. / Li, Z.K. / Cui, Z.L. / Liu, W.D.
History
DepositionAug 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PnpA
B: PnpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0423
Polymers93,2562
Non-polymers7861
Water1,33374
1
A: PnpA


Theoretical massNumber of molelcules
Total (without water)46,6281
Polymers46,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16810 Å2
MethodPISA
2
B: PnpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4142
Polymers46,6281
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.433, 77.177, 210.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 9 - 402 / Label seq-ID: 9 - 402

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein PnpA / p-Nitrophenol 4-monooxygenase


Mass: 46628.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: DLL-E4 / Gene: pnpA / Production host: Escherichia coli (E. coli) / References: UniProt: C6FI48
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% isopropanol, 0.1M Tris-HCl, pH 8.5, 13.5 % (w/v) PEG 4000, 5% glycerol, 0.01mM FAD, 0.5mM PNP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.5397 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5397 Å / Relative weight: 1
ReflectionResolution: 2.48→30 Å / Num. obs: 32252 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.37
Reflection shellResolution: 2.48→2.57 Å / Rmerge(I) obs: 0.493 / Num. unique obs: 3154

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IHG

3ihg


Resolution: 2.48→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.376 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.281 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24576 1558 4.8 %RANDOM
Rwork0.19352 ---
obs0.1961 30628 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.655 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0 Å20 Å2
2--1.75 Å20 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6147 0 53 74 6274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196341
X-RAY DIFFRACTIONr_bond_other_d0.0050.026064
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9668612
X-RAY DIFFRACTIONr_angle_other_deg1.118313886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52222.746295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.571151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8261565
X-RAY DIFFRACTIONr_chiral_restr0.0860.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217163
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021483
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_it3.6324.4923133
X-RAY DIFFRACTIONr_mcbond_other3.6314.4913132
X-RAY DIFFRACTIONr_mcangle_it5.3696.733911
X-RAY DIFFRACTIONr_mcangle_other5.3696.7313912
X-RAY DIFFRACTIONr_scbond_it4.9365.1363208
X-RAY DIFFRACTIONr_scbond_other4.9365.1363209
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8327.4354702
X-RAY DIFFRACTIONr_long_range_B_refined11.55243.66826340
X-RAY DIFFRACTIONr_long_range_B_other11.55443.66826331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 22405 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.478→2.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 94 -
Rwork0.24 2066 -
obs--93.71 %

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