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- PDB-6vjx: The crystal structure of 4-isobutylbenzoic acid-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6vjx
TitleThe crystal structure of 4-isobutylbenzoic acid-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / enzyme / biocatalysis / bioengineering / 4-methoxycinnamic acid / P450 / substrate / metabolism
Function / homology
Function and homology information


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, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 4-(2-methylpropyl)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.788 Å
AuthorsDoherty, Z.D. / Bell, S.G. / Bruning, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: The crystal structure of 4-isobutylbenzoic acid-bound CYP199A4
Authors: Doherty, Z.D. / Bell, S.G. / Bruning, J.
History
DepositionJan 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7294
Polymers42,8991
Non-polymers8303
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-37 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.417, 51.428, 79.415
Angle α, β, γ (deg.)90.000, 91.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 42898.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IU02
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-QZP / 4-(2-methylpropyl)benzoic acid / 4-isobutylbenzoic acid


Mass: 178.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium acetate, 15-30% w/v PEG3350, 0.1 M Bis-Tris, pH 5-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.788→43.16 Å / Num. obs: 30918 / % possible obs: 97.5 % / Redundancy: 7 % / Biso Wilson estimate: 12.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.036 / Rrim(I) all: 0.097 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.79-1.826.90.3891145416570.9230.1590.4213.592.5
9.12-43.166.50.04517062640.9980.0190.04932.498.9

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5KBD

5kbd


Resolution: 1.788→43.16 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 16.91
RfactorNum. reflection% reflection
Rfree0.1788 1996 6.46 %
Rwork0.133 --
obs0.1359 30903 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.62 Å2 / Biso mean: 14.0224 Å2 / Biso min: 4.38 Å2
Refinement stepCycle: final / Resolution: 1.788→43.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 57 486 3564
Biso mean--10 23.98 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013168
X-RAY DIFFRACTIONf_angle_d1.0734328
X-RAY DIFFRACTIONf_chiral_restr0.062470
X-RAY DIFFRACTIONf_plane_restr0.007574
X-RAY DIFFRACTIONf_dihedral_angle_d9.3622606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.788-1.83270.23191410.1587194993
1.8327-1.88220.20221450.1432202396
1.8822-1.93760.20821370.141203397
1.9376-2.00020.18471330.1321204696
2.0002-2.07170.17991430.1254203596
2.0717-2.15460.18651360.1295205698
2.1546-2.25270.18531460.1317205298
2.2527-2.37140.18681450.128205897
2.3714-2.520.21391430.1367206898
2.52-2.71450.19331450.1426208298
2.7145-2.98760.18251420.1449210398
2.9876-3.41980.16171440.1323210799
3.4198-4.30790.14381450.115210599
4.3079-43.160.16081510.1339219099

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