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- PDB-9g9s: Crystal structure of PbdA bound to veratrate -

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Basic information

Entry
Database: PDB / ID: 9g9s
TitleCrystal structure of PbdA bound to veratrate
ComponentsCytochrome P450 CYP199
KeywordsOXIDOREDUCTASE / Cytochrome P450
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 3,4-dimethoxybenzoic acid / Cytochrome P450 CYP199
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHinchen, D.J. / Wolf, M.E. / Eltis, L.D. / McGeehan, J.E.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Research EnglandE3 Funding United Kingdom
Department of Energy (DOE, United States)DE-AC36-08GO28308 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Characterization of a cytochrome P450 that catalyzes the O-demethylation of lignin-derived benzoates.
Authors: Wolf, M.E. / Hinchen, D.J. / McGeehan, J.E. / Eltis, L.D.
History
DepositionJul 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 CYP199
B: Cytochrome P450 CYP199
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7278
Polymers91,9452
Non-polymers1,7826
Water8,791488
1
A: Cytochrome P450 CYP199
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7713
Polymers45,9731
Non-polymers7992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 CYP199
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9555
Polymers45,9731
Non-polymers9834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.999, 55.357, 64.693
Angle α, β, γ (deg.)98.676, 95.002, 99.014
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cytochrome P450 CYP199


Mass: 45972.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: RHA1_ro02948 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0SCI3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-TWO / 3,4-dimethoxybenzoic acid / VERATRIC ACID


Mass: 182.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M Sodium phosphate, 0.8 M Potassium phosphate, 0.1 M HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→63.54 Å / Num. obs: 57209 / % possible obs: 97.6 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.129 / Rrim(I) all: 0.182 / Χ2: 0.94 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.06-63.543.60.03517.24950.9910.0350.050.5699.4
1.85-1.893.51.1090.934780.4121.1091.5680.9695.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→63.54 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.052 / SU ML: 0.173 / Cross valid method: FREE R-VALUE / ESU R: 0.194 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.258 2837 4.961 %
Rwork0.2078 54352 -
all0.21 --
obs-57189 97.491 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.936 Å2
Baniso -1Baniso -2Baniso -3
1--0.602 Å2-0.588 Å20.907 Å2
2--0.832 Å20.348 Å2
3----0.397 Å2
Refinement stepCycle: LAST / Resolution: 1.85→63.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6053 0 124 488 6665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126383
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165901
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.8238757
X-RAY DIFFRACTIONr_angle_other_deg0.5991.75713484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1425790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.23565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6810896
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.19810298
X-RAY DIFFRACTIONr_chiral_restr0.0830.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027891
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021581
X-RAY DIFFRACTIONr_nbd_refined0.2240.21494
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.25842
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23134
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2516
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0420.25
X-RAY DIFFRACTIONr_metal_ion_refined0.060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.223
X-RAY DIFFRACTIONr_nbd_other0.1950.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.228
X-RAY DIFFRACTIONr_mcbond_it2.0322.3843157
X-RAY DIFFRACTIONr_mcbond_other2.0322.3843157
X-RAY DIFFRACTIONr_mcangle_it2.9474.2793948
X-RAY DIFFRACTIONr_mcangle_other2.9474.283949
X-RAY DIFFRACTIONr_scbond_it2.3182.5543226
X-RAY DIFFRACTIONr_scbond_other2.3172.5543227
X-RAY DIFFRACTIONr_scangle_it3.5494.5964809
X-RAY DIFFRACTIONr_scangle_other3.5494.5964810
X-RAY DIFFRACTIONr_lrange_it5.0926.0227625
X-RAY DIFFRACTIONr_lrange_other4.92325.3487467
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.3361930.32540410.32544140.890.91195.92210.33
1.898-1.950.332050.29138040.29341650.9190.93696.25450.295
1.95-2.0060.2982010.2737620.27140930.9340.94696.82380.272
2.006-2.0680.2981900.24736940.24940080.940.95596.90620.247
2.068-2.1360.2991840.24236000.24538990.9260.95997.05050.24
2.136-2.2110.2491950.20434300.20737320.9560.97197.13290.199
2.211-2.2940.2721620.19833430.20236010.9480.97297.33410.192
2.294-2.3880.2711600.19932110.20234800.9490.97496.86780.19
2.388-2.4940.3151660.20430460.2132960.9340.97297.45150.196
2.494-2.6150.2661650.229730.20331990.9530.97498.09320.192
2.615-2.7560.2581330.19928420.20230310.960.97598.15240.19
2.756-2.9230.3161320.20226950.20728790.9360.97298.19380.192
2.923-3.1250.261310.19825050.20226710.9560.97498.68960.19
3.125-3.3740.2481200.18823630.19125180.960.97798.610.181
3.374-3.6950.2221180.19121550.19322990.9630.97698.86910.186
3.695-4.130.2141100.18619520.18720830.9690.97798.99180.183
4.13-4.7650.2171040.15616890.15918420.9620.98297.33990.156
4.765-5.8280.202860.19814630.19815580.9750.97799.42230.201
5.828-8.2070.276550.21811460.22112060.9610.96899.58540.219
8.207-63.540.181270.2166380.2156700.9810.96499.25370.215

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