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- PDB-9g9r: Crystal structure of PbdA bound to p-ethylbenzoate -

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Basic information

Entry
Database: PDB / ID: 9g9r
TitleCrystal structure of PbdA bound to p-ethylbenzoate
ComponentsCytochrome P450 CYP199
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Lignin
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
4-ethylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 CYP199
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)93,93911
Polymers91,9452
Non-polymers1,9949
Water8,179454
1
A: Cytochrome P450 CYP199
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2008
Polymers45,9731
Non-polymers1,2277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 CYP199
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7393
Polymers45,9731
Non-polymers7672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.751, 54.437, 64.018
Angle α, β, γ (deg.)99.541, 95.379, 102.644
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-EGM / 4-ethylbenzoic acid


Mass: 150.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 454 / 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

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 pH 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 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: 1.65→52.13 Å / Num. obs: 77677 / % possible obs: 96.9 % / Redundancy: 3.1 % / CC1/2: 0.976 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.091 / Rrim(I) all: 0.129 / Χ2: 0.88 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.89-52.133.50.015315130.8730.0150.0220.3899.4
1.65-1.683.31.6140.738870.3451.6142.2830.8895.2

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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: 1.65→52.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.573 / SU ML: 0.138 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2467 3907 5.035 %
Rwork0.1941 73685 -
all0.197 --
obs-77592 96.784 %
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: 25.693 Å2
Baniso -1Baniso -2Baniso -3
1-1.836 Å2-1.113 Å22.234 Å2
2---1.405 Å2-1.172 Å2
3---0.127 Å2
Refinement stepCycle: LAST / Resolution: 1.65→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6047 0 138 454 6639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165936
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.8218846
X-RAY DIFFRACTIONr_angle_other_deg0.6081.75413567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.233562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3210891
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.49210300
X-RAY DIFFRACTIONr_chiral_restr0.0850.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028000
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021596
X-RAY DIFFRACTIONr_nbd_refined0.2270.21564
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25925
X-RAY DIFFRACTIONr_nbtor_refined0.1860.23206
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23331
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2415
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1750.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.239
X-RAY DIFFRACTIONr_nbd_other0.1760.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.231
X-RAY DIFFRACTIONr_mcbond_it2.2032.4083194
X-RAY DIFFRACTIONr_mcbond_other2.2032.4083194
X-RAY DIFFRACTIONr_mcangle_it3.1364.3174003
X-RAY DIFFRACTIONr_mcangle_other3.1364.3174004
X-RAY DIFFRACTIONr_scbond_it2.8962.6673246
X-RAY DIFFRACTIONr_scbond_other2.8962.6673247
X-RAY DIFFRACTIONr_scangle_it4.4234.7584843
X-RAY DIFFRACTIONr_scangle_other4.4224.7584844
X-RAY DIFFRACTIONr_lrange_it5.72928.0727662
X-RAY DIFFRACTIONr_lrange_other5.67127.2047559
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
1.65-1.6930.3632540.36253410.36259190.8590.87994.52610.372
1.693-1.7390.3472720.34252170.34257720.8910.89495.0970.35
1.739-1.7890.3042770.31551330.31556450.9210.90795.8370.32
1.789-1.8440.3182430.29349670.29454290.9140.91895.96610.292
1.844-1.9050.2922490.26647980.26752760.9260.93895.65960.261
1.905-1.9720.2792410.24247070.24451240.9360.9596.56520.234
1.972-2.0460.292120.21545500.21849240.9410.96196.710.202
2.046-2.1290.2452600.19643460.19847610.9580.96996.74440.182
2.129-2.2240.2632660.19241740.19645720.9510.97297.11290.179
2.224-2.3320.2562200.18339900.18743490.9590.97696.80390.169
2.332-2.4580.2642240.17938180.18441750.9610.97996.81440.166
2.458-2.6070.261740.17536410.17938940.9590.98197.97120.162
2.607-2.7860.2351620.16934200.17236650.9680.98297.73530.158
2.786-3.0090.2311830.15932090.16334410.9690.98498.5760.149
3.009-3.2950.2281660.17229280.17531350.9680.98298.69220.164
3.295-3.6820.2131320.15627000.15928660.9740.98598.81370.153
3.682-4.2480.2051280.15223610.15525220.9750.98698.69150.153
4.248-5.1940.2021190.1519510.15321190.9740.98797.68760.152
5.194-7.310.206790.17715600.17916480.9740.98299.45390.179
7.31-52.130.25460.198740.1939230.9690.98299.6750.196

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