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- PDB-5u6t: The crystal structure of 4-ethoxybenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 5u6t
TitleThe crystal structure of 4-ethoxybenzoate-bound 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-ethoxybenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.935 Å
AuthorsColeman, T. / Bruning, J.B. / Bell, S.G.
CitationJournal: Acs Catalysis / Year: 2018
Title: Cytochrome P450 CYP199A4 from Rhodopseudomonas palustris Catalyzes Heteroatom Dealkylations, Sulfoxidation, and Amide and Cyclic Hemiacetal Formation
Authors: Coleman, T. / Wong, S.H. / Podgorski, M.N. / Bruning, J.B. / De Voss, J.J. / Bell, S.G.
History
DepositionDec 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 4, 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)43,7174
Polymers42,8991
Non-polymers8183
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.445, 51.421, 79.116
Angle α, β, γ (deg.)90.000, 91.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 42898.660 Da / Num. of mol.: 1 / Fragment: UNP residues 18-410
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-81J / 4-ethoxybenzoic acid


Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3
#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.: 349 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: PEG 3350: 29% w/v MgAc: 0.2M Bis-Tris pH 5.75, 0.1M 1mM 4-ethoxybenzoic acid in 35mg/mL protein
PH range: 5 - 5.75 / Temp details: 16 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.94→44.42 Å / Num. obs: 26777 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 15.41 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.066 / Rrim(I) all: 0.18 / Net I/σ(I): 8.4 / Num. measured all: 199377 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.94-1.987.20.7881234917110.7740.3120.8492.196.9
9.08-44.426.50.05818442850.9960.0240.06325.799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.01 Å44.05 Å
Translation2.01 Å44.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimless0.5.25data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KDB

5kdb


Resolution: 1.935→44.419 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 1400 5.23 %Random
Rwork0.1331 25363 --
obs0.1358 26763 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.91 Å2 / Biso mean: 18.9128 Å2 / Biso min: 6.21 Å2
Refinement stepCycle: final / Resolution: 1.935→44.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 95 349 3465
Biso mean--12.4 25.71 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123155
X-RAY DIFFRACTIONf_angle_d1.3834308
X-RAY DIFFRACTIONf_chiral_restr0.051468
X-RAY DIFFRACTIONf_plane_restr0.007571
X-RAY DIFFRACTIONf_dihedral_angle_d13.8221157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9354-2.00450.2521370.18312460259798
2.0045-2.08480.22861520.172224882640100
2.0848-2.17970.28141080.155125412649100
2.1797-2.29460.22791440.145825502694100
2.2946-2.43830.20141250.13525552680100
2.4383-2.62660.20961310.133325502681100
2.6266-2.89090.17271600.132424872647100
2.8909-3.30910.17551590.128525372696100
3.3091-4.16860.15381450.106825612706100
4.1686-44.4310.12841390.121826342773100

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