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- PDB-9zeh: The 150-K crystal structure of CYP199A4 bound to 4-phenoxybenzoic... -

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Basic information

Entry
Database: PDB / ID: 9zeh
TitleThe 150-K crystal structure of CYP199A4 bound to 4-phenoxybenzoic acid (dataset 2; 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: 1.512 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
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.419, 51.556, 79.018
Angle α, β, γ (deg.)90.00, 92.20, 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-JO4 / 4-phenoxybenzoic acid


Mass: 214.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O3 / 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.: 511 / 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: 2.03 Å3/Da / Density % sol: 39.34 %
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: 150 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: 1.51→44.39 Å / Num. obs: 55691 / % possible obs: 99.1 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.047 / Rrim(I) all: 0.123 / Χ2: 0.5 / Net I/σ(I): 9.4 / Num. measured all: 376071
Reflection shellResolution: 1.51→1.54 Å / % possible obs: 86.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.854 / Num. measured all: 15811 / Num. unique obs: 2400 / CC1/2: 0.526 / Rpim(I) all: 0.77 / Rrim(I) all: 2.013 / Χ2: 0.42 / Net I/σ(I) obs: 0.9

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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: 1.512→43.169 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 2001 3.6 %
Rwork0.1594 --
obs0.1604 55592 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.512→43.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 60 511 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123233
X-RAY DIFFRACTIONf_angle_d1.1834425
X-RAY DIFFRACTIONf_dihedral_angle_d25.1741194
X-RAY DIFFRACTIONf_chiral_restr0.072479
X-RAY DIFFRACTIONf_plane_restr0.009591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5122-1.550.29591450.29743613X-RAY DIFFRACTION95
1.55-1.5920.31581320.26953826X-RAY DIFFRACTION100
1.592-1.63880.25441540.24393799X-RAY DIFFRACTION100
1.6388-1.69170.2261270.22143813X-RAY DIFFRACTION100
1.6917-1.75220.26121420.21023836X-RAY DIFFRACTION100
1.7522-1.82230.22851500.19623808X-RAY DIFFRACTION100
1.8223-1.90530.23121440.17823825X-RAY DIFFRACTION100
1.9053-2.00570.19731390.16943859X-RAY DIFFRACTION100
2.0057-2.13140.20381430.16433812X-RAY DIFFRACTION99
2.1314-2.29590.19731470.15123823X-RAY DIFFRACTION100
2.2959-2.52690.17011410.15053850X-RAY DIFFRACTION100
2.5269-2.89250.16831470.14913867X-RAY DIFFRACTION100
2.8925-3.6440.16021440.1363896X-RAY DIFFRACTION100
3.644-43.1690.13981460.12723964X-RAY DIFFRACTION100

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