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- PDB-9mje: The 200-K crystal structure of CYP199A4 bound to 3-methylaminoben... -

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Basic information

Entry
Database: PDB / ID: 9mje
TitleThe 200-K crystal structure of CYP199A4 bound to 3-methylaminobenzoic acid (dataset 3, increasing temperature series)
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Variable-temperature X-ray 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 / 3-(methylamino)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionDec 14, 2024Deposition 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)45,3914
Polymers44,5871
Non-polymers8033
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.670, 51.696, 79.699
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-OW4 / 3-(methylamino)benzoic acid


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2 / 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.: 445 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
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: 200 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: Apr 7, 2022
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: 1.95→43.362 Å / Num. obs: 26650 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.059 / Rrim(I) all: 0.148 / Χ2: 1.01 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2 Å / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.721 / Num. measured all: 12138 / Num. unique obs: 1840 / CC1/2: 0.937 / Rpim(I) all: 0.301 / Rrim(I) all: 0.782 / Χ2: 0.97 / Net I/σ(I) obs: 6.3

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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: 1.95→43.362 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 1352 5.08 %
Rwork0.1542 --
obs0.156 26622 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→43.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 55 445 3521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043218
X-RAY DIFFRACTIONf_angle_d0.7194404
X-RAY DIFFRACTIONf_dihedral_angle_d23.0331190
X-RAY DIFFRACTIONf_chiral_restr0.045476
X-RAY DIFFRACTIONf_plane_restr0.004589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01970.26641330.17822486X-RAY DIFFRACTION100
2.0197-2.10060.2261360.17252497X-RAY DIFFRACTION100
2.1006-2.19620.25321250.17062502X-RAY DIFFRACTION100
2.1962-2.31190.20031270.16532524X-RAY DIFFRACTION100
2.3119-2.45680.21841240.16722543X-RAY DIFFRACTION100
2.4568-2.64640.20271540.17062503X-RAY DIFFRACTION100
2.6464-2.91270.21471450.17752496X-RAY DIFFRACTION100
2.9127-3.33410.24271370.16732543X-RAY DIFFRACTION100
3.3341-4.20.14181410.132555X-RAY DIFFRACTION100
4.2-43.3620.12831300.12682621X-RAY DIFFRACTION100

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