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- PDB-6c3j: The crystal structure of 4-(thiophen-3-yl)benzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6c3j
TitleThe crystal structure of 4-(thiophen-3-yl)benzoate-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-(thiophen-3-yl)benzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 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: The crystal structure of 4-(thiophen-3-yl)benzoate-bound CYP199A4
Authors: Coleman, T. / Bruning, J.B. / Bell, S.G.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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)43,7554
Polymers42,8991
Non-polymers8563
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.283, 51.580, 79.450
Angle α, β, γ (deg.)90.000, 92.020, 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
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-EJD / 4-(thiophen-3-yl)benzoic acid


Mass: 204.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O2S
#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.: 571 / 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: 41.81 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2M MgAc 0.1M Bis-Tris, pH 5.5 23 % w/v PEG-3350 / PH range: 5.25-6.0 / Temp details: 16 C

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→44.26 Å / Num. obs: 41408 / % possible obs: 97.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 14.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.039 / Rrim(I) all: 0.108 / Net I/σ(I): 11.8 / Num. measured all: 315104
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.66-1.697.50.78616740.8020.3060.84580.6
9.08-44.266.40.032770.9990.0120.03297.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.73 Å43.25 Å
Translation5.73 Å43.25 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVB

5uvb


Resolution: 1.66→33.587 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.55
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 2087 5.04 %Random selection.
Rwork0.1584 ---
obs0.1603 41401 97.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.21 Å2 / Biso mean: 17.8321 Å2 / Biso min: 7.48 Å2
Refinement stepCycle: final / Resolution: 1.66→33.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 58 571 3650
Biso mean--12.78 28.18 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073162
X-RAY DIFFRACTIONf_angle_d1.14320
X-RAY DIFFRACTIONf_chiral_restr0.045469
X-RAY DIFFRACTIONf_plane_restr0.006573
X-RAY DIFFRACTIONf_dihedral_angle_d23.0061160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6583-1.69680.26781280.22492267239585
1.6968-1.73930.26731380.2212566270497
1.7393-1.78630.25531350.19082624275997
1.7863-1.83890.22871360.19132598273497
1.8389-1.89820.23471370.18232607274497
1.8982-1.9660.23521110.19322622273398
1.966-2.04480.21991180.17222669278798
2.0448-2.13780.20621830.16522580276398
2.1378-2.25050.20741340.16112660279498
2.2505-2.39140.19491650.15722609277499
2.3914-2.5760.1731460.15412656280298
2.576-2.83510.20611370.15882684282199
2.8351-3.24510.20191340.15212691282599
3.2451-4.08740.15511560.13112696285299
4.0874-33.5940.16321290.13622785291499

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