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- PDB-6oow: The crystal structure of 4-ethylbenzoate bound to T252A mutant of... -

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Basic information

Entry
Database: PDB / ID: 6oow
TitleThe crystal structure of 4-ethylbenzoate bound to T252A mutant of CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450 / 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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-ethylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsColeman, T. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: To Be Published
Title: Structural investigation of the interplay between the substrate and the acid-alcohol pair of residues in cytochrome P450 enzymes
Authors: Coleman, T. / Bruning, J.B. / Bell, S.G.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,6714
Polymers42,8691
Non-polymers8023
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-37 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.030, 51.410, 79.140
Angle α, β, γ (deg.)90.000, 92.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 42868.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IU02
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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-EGM / 4-ethylbenzoic acid


Mass: 150.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 36.79 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 23% w/v PEG3350, 0.2 M magnesium acetate tetrahydrate
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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→43.1 Å / Num. obs: 35102 / % possible obs: 81.7 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Net I/σ(I): 15.8 / Num. measured all: 230643 / Scaling rejects: 152
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.636.60.2761076316380.9470.1140.2995.974
8.62-43.17.50.07417262300.9920.0290.0830.584.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.43 Å32.06 Å
Translation5.43 Å32.06 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DO1

4do1


Resolution: 1.6→32.056 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.37
RfactorNum. reflection% reflectionSelection details
Rfree0.168 1695 4.83 %Random selection
Rwork0.1424 ---
obs0.1436 35097 80.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.03 Å2 / Biso mean: 11.0462 Å2 / Biso min: 1.09 Å2
Refinement stepCycle: final / Resolution: 1.6→32.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 55 562 3636
Biso mean--5.15 21.74 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053176
X-RAY DIFFRACTIONf_angle_d0.8314341
X-RAY DIFFRACTIONf_chiral_restr0.045470
X-RAY DIFFRACTIONf_plane_restr0.005578
X-RAY DIFFRACTIONf_dihedral_angle_d17.2851897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.64710.21161350.16642526266173
1.6471-1.70020.20431260.16292515264174
1.7002-1.7610.22821350.16632512264773
1.761-1.83150.22261200.16052528264874
1.8315-1.91490.19051220.15932550267274
1.9149-2.01580.19941420.15382675281777
2.0158-2.14210.18981380.14472743288179
2.1421-2.30740.17991410.14082900304184
2.3074-2.53950.14671610.13893079324089
2.5395-2.90680.17031760.14123134331091
2.9068-3.66140.14011560.12853138329490
3.6614-32.06270.11711430.12833102324587

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