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- PDB-9doe: The high-resolution crystal structure of WT CYP199A4 bound to 4-m... -

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Basic information

Entry
Database: PDB / ID: 9doe
TitleThe high-resolution crystal structure of WT CYP199A4 bound to 4-methoxybenzoic acid at 100 K
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / CYP199A4 / substrate
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
4-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.265 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: The high-resolution crystal structure of WT CYP199A4 bound to 4-methoxybenzoic acid at 100 K
Authors: Podgorski, M.N. / Bell, S.G.
History
DepositionSep 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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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)45,3924
Polymers44,5871
Non-polymers8043
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-30 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.465, 51.387, 79.052
Angle α, β, γ (deg.)90.00, 92.34, 90.00
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 HaA2 (phototrophic)
Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 694 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM Bis-Tris (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate, 20-32% PEG3350
PH range: 5.00-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2021
RadiationMonochromator: Double-crystal Si(111) liquid nitrogen cooled (DC) or channel-cut Si(111) liquid nitrogen cooled (CC)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.26→44.43 Å / Num. obs: 94087 / % possible obs: 98.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Χ2: 0.5 / Net I/σ(I): 8.9 / Num. measured all: 627512
Reflection shellResolution: 1.26→1.29 Å / % possible obs: 81.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 1.046 / Num. measured all: 23852 / Num. unique obs: 3840 / CC1/2: 0.7 / Rpim(I) all: 0.447 / Rrim(I) all: 1.141 / Χ2: 0.36 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.265→43.074 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 1993 2.12 %
Rwork0.1591 --
obs0.1594 94006 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.265→43.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 55 694 3770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043238
X-RAY DIFFRACTIONf_angle_d0.8624431
X-RAY DIFFRACTIONf_dihedral_angle_d24.8391201
X-RAY DIFFRACTIONf_chiral_restr0.074479
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2654-1.2970.28241300.26355961X-RAY DIFFRACTION90
1.297-1.33210.24761310.23776638X-RAY DIFFRACTION100
1.3321-1.37130.21971520.22376603X-RAY DIFFRACTION100
1.3713-1.41550.2111400.20866592X-RAY DIFFRACTION100
1.4155-1.46610.20971460.19266575X-RAY DIFFRACTION100
1.4661-1.52480.20731380.17676578X-RAY DIFFRACTION100
1.5248-1.59420.20871470.17246596X-RAY DIFFRACTION99
1.5942-1.67830.20471420.16726584X-RAY DIFFRACTION99
1.6783-1.78340.20381470.1666608X-RAY DIFFRACTION99
1.7834-1.92110.19121310.16326551X-RAY DIFFRACTION99
1.9211-2.11450.17231420.15516605X-RAY DIFFRACTION99
2.1145-2.42040.14781480.14156649X-RAY DIFFRACTION100
2.4204-3.04940.17691450.14776678X-RAY DIFFRACTION100
3.0494-43.0740.13961540.13146795X-RAY DIFFRACTION100

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