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- PDB-9zeg: The 100-K crystal structure of CYP199A4 bound to 4-phenoxybenzoic... -

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Basic information

Entry
Database: PDB / ID: 9zeg
TitleThe 100-K crystal structure of CYP199A4 bound to 4-phenoxybenzoic acid (dataset 1; increasing temperature series)
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / variable-temperature crystallography
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-phenoxybenzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.532 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Chem Sci / Year: 2026
Title: Structural basis for substrate-dependent allostery in oxygen activation by a cytochrome P450 enzyme revealed by analysis at different temperatures
Authors: Podgorski, M.N. / McDougal, D.P. / Campbell, E.C. / Bruning, J.B. / Bell, S.G.
History
DepositionNov 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: 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)45,4544
Polymers44,5871
Non-polymers8663
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.350, 51.466, 78.922
Angle α, β, γ (deg.)90.00, 92.19, 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-JO4 / 4-phenoxybenzoic acid


Mass: 214.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O3 / 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.: 516 / 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: 39.07 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: The crystallization buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350
PH range: 5.0-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 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: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.53→44.32 Å / Num. obs: 53240 / % possible obs: 98.8 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.059 / Rrim(I) all: 0.154 / Χ2: 0.49 / Net I/σ(I): 9.2 / Num. measured all: 357151
Reflection shellResolution: 1.53→1.56 Å / % possible obs: 87.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 2.015 / Num. measured all: 15462 / Num. unique obs: 2292 / CC1/2: 0.53 / Rpim(I) all: 0.828 / Rrim(I) all: 2.183 / Χ2: 0.41 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.532→43.1 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 1981 3.73 %
Rwork0.171 --
obs0.1721 53133 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.532→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 60 516 3597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063226
X-RAY DIFFRACTIONf_angle_d0.8514414
X-RAY DIFFRACTIONf_dihedral_angle_d9.4582631
X-RAY DIFFRACTIONf_chiral_restr0.051477
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.532-1.56990.33131340.30133506X-RAY DIFFRACTION96
1.5699-1.61230.32691430.27223608X-RAY DIFFRACTION99
1.6123-1.65980.28221360.25543662X-RAY DIFFRACTION99
1.6598-1.71330.311370.2513630X-RAY DIFFRACTION99
1.7133-1.77460.28881420.23993594X-RAY DIFFRACTION98
1.7746-1.84560.27231410.22133614X-RAY DIFFRACTION98
1.8456-1.92960.23411400.19343648X-RAY DIFFRACTION99
1.9296-2.03130.21271400.19553646X-RAY DIFFRACTION100
2.0313-2.15860.24581430.19213666X-RAY DIFFRACTION100
2.1586-2.32530.20441450.17053676X-RAY DIFFRACTION100
2.3253-2.55930.19881450.1583690X-RAY DIFFRACTION100
2.5593-2.92950.17011400.15293711X-RAY DIFFRACTION100
2.9295-3.69060.1511480.13713718X-RAY DIFFRACTION100
3.6906-43.10.14711470.12993783X-RAY DIFFRACTION100

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