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- PDB-9dx9: The crystal structure of F182AQE CYP199A4 bound to 4-t-butylbenzo... -

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Basic information

Entry
Database: PDB / ID: 9dx9
TitleThe crystal structure of F182AQE CYP199A4 bound to 4-t-butylbenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 peroxygenase / hydroxylation
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-~{tert}-butylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Acs Catalysis / Year: 2025
Title: Comparing and Combining Alternative Strategies for Enhancing Cytochrome P450 Peroxygenase Activity
Authors: Podgorski, M.N. / Bell, S.G.
History
DepositionOct 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 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)45,4075
Polymers44,5521
Non-polymers8544
Water11,818656
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-40 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.809, 51.361, 78.378
Angle α, β, γ (deg.)90.00, 93.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44552.387 Da / Num. of mol.: 1 / Mutation: F182A, D251Q, T252E
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

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Non-polymers , 5 types, 660 molecules

#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-5R0 / 4-~{tert}-butylbenzoic acid


Mass: 178.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14O2 / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 39.12 %
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: 5.0-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2023
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: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.52→42.934 Å / Num. obs: 54723 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Χ2: 0.52 / Net I/σ(I): 15.9
Reflection shellResolution: 1.52→1.55 Å / % possible obs: 94.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.324 / Num. measured all: 16802 / Num. unique obs: 2540 / CC1/2: 0.953 / Rpim(I) all: 0.134 / Rrim(I) all: 0.351 / Χ2: 0.47 / Net I/σ(I) obs: 3.7

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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: 1.52→42.934 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1656 2024 3.7 %
Rwork0.1433 --
obs0.1441 54699 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→42.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 58 656 3732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063350
X-RAY DIFFRACTIONf_angle_d0.8894602
X-RAY DIFFRACTIONf_dihedral_angle_d24.5421250
X-RAY DIFFRACTIONf_chiral_restr0.052493
X-RAY DIFFRACTIONf_plane_restr0.006621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.55790.25481380.21223590X-RAY DIFFRACTION96
1.5579-1.60010.23591500.18553768X-RAY DIFFRACTION100
1.6001-1.64710.20611430.16063726X-RAY DIFFRACTION100
1.6471-1.70030.19251340.14523773X-RAY DIFFRACTION100
1.7003-1.76110.16231480.14433727X-RAY DIFFRACTION100
1.7611-1.83160.17391420.14153769X-RAY DIFFRACTION100
1.8316-1.91490.18391420.14553753X-RAY DIFFRACTION100
1.9149-2.01590.18411440.15293761X-RAY DIFFRACTION100
2.0159-2.14220.16161450.14533795X-RAY DIFFRACTION100
2.1422-2.30760.16251490.14363751X-RAY DIFFRACTION100
2.3076-2.53980.17451460.14463787X-RAY DIFFRACTION100
2.5398-2.90720.18351440.14463778X-RAY DIFFRACTION100
2.9072-3.66250.14111480.13223811X-RAY DIFFRACTION100
3.6625-42.9340.1331510.12963886X-RAY DIFFRACTION100

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