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- PDB-7jxb: The crystal structure of 4-(3'-methoxyphenyl)benzoic acid-bound C... -

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Basic information

Entry
Database: PDB / ID: 7jxb
TitleThe crystal structure of 4-(3'-methoxyphenyl)benzoic acid-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / Monooxygenase / Heme / Oxygen Insertion
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 / 3'-methoxy[1,1'-biphenyl]-4-carboxylic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.655 Å
AuthorsDoherty, D.Z. / Bell, S.G. / Bruning, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Chemistry / Year: 2022
Title: Enabling Aromatic Hydroxylation in a Cytochrome P450 Monooxygenase Enzyme through Protein Engineering.
Authors: Coleman, T. / Lee, J.Z.H. / Kirk, A.M. / Doherty, D.Z. / Podgorski, M.N. / Pinidiya, D.K. / Bruning, J.B. / De Voss, J.J. / Krenske, E.H. / Bell, S.G.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4684
Polymers44,5871
Non-polymers8803
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-37 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.070, 51.390, 79.410
Angle α, β, γ (deg.)90.000, 92.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44587.430 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 BL21(DE3) (bacteria) / References: UniProt: Q2IU02
#2: Chemical ChemComp-VLG / 3'-methoxy[1,1'-biphenyl]-4-carboxylic acid / 4-(3'-methoxyphenyl)benzoic acid


Mass: 228.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 519 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.88 Å3/Da / Density % sol: 34.51 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium acetate, 100 mM Bis-Tris (adjusted with acetic acid to pH 5.0-5.75), 20-32% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.655→43.14 Å / Num. obs: 39399 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 8.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.06 / Net I/σ(I): 26.3
Reflection shellResolution: 1.66→1.68 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.186 / Num. unique obs: 1875 / CC1/2: 0.983 / Rpim(I) all: 0.077 / Rrim(I) all: 0.201 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 1.655→43.136 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.166 2017 5.12 %
Rwork0.1335 37365 -
obs0.1352 39382 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.36 Å2 / Biso mean: 10.8247 Å2 / Biso min: 1.64 Å2
Refinement stepCycle: final / Resolution: 1.655→43.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 61 519 3601
Biso mean--5.52 21.37 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083162
X-RAY DIFFRACTIONf_angle_d1.0764317
X-RAY DIFFRACTIONf_chiral_restr0.054468
X-RAY DIFFRACTIONf_plane_restr0.007572
X-RAY DIFFRACTIONf_dihedral_angle_d11.1571882
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.655-1.69640.20411360.1377258998
1.6964-1.74230.21371210.138263799
1.7423-1.79360.18381380.1326267399
1.7936-1.85150.17351550.1306264599
1.8515-1.91760.15131310.1355262499
1.9176-1.99440.1691460.1278268499
1.9944-2.08520.19191350.12452659100
2.0852-2.19510.16921440.13592681100
2.1951-2.33260.16441490.1322647100
2.3326-2.51270.16781720.13952648100
2.5127-2.76550.15581510.13952709100
2.7655-3.16560.17931600.14152681100
3.1656-3.98790.14591280.1232715100
3.9879-43.1360.14511510.13562773100

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