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- PDB-6wfl: Camphor soaked P450cam D251E -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6wfl
TitleCamphor soaked P450cam D251E
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / P450cam / D251E / camphor / PdX / PdR
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm
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
5-EXO-HYDROXYCAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAmaya, J.A. / Poulos, T.L. / Batabyal, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131920 United States
CitationJournal: Biochemistry / Year: 2020
Title: Proton Relay Network in the Bacterial P450s: CYP101A1 and CYP101D1.
Authors: Amaya, J.A. / Batabyal, D. / Poulos, T.L.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5584
Polymers46,7341
Non-polymers8243
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.324, 64.039, 105.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Camphor 5-monooxygenase / / Cytochrome P450-cam / Cytochrome P450cam


Mass: 46734.102 Da / Num. of mol.: 1 / Mutation: D251E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli (E. coli) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CAH / 5-EXO-HYDROXYCAMPHOR


Mass: 168.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris pH 6.5, 20% PEG 8000, 200 mM potassium chloride, 5 mM DTT

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→34.25 Å / Num. obs: 114317 / % possible obs: 98.98 % / Redundancy: 2 % / Biso Wilson estimate: 23.78 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.01
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 57198 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WK7

5wk7


Resolution: 1.6→34.25 Å / SU ML: 0.2687 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3579
RfactorNum. reflection% reflection
Rfree0.2538 1101 1.94 %
Rwork0.2177 --
obs0.2184 56807 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 12 266 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713351
X-RAY DIFFRACTIONf_angle_d0.98264573
X-RAY DIFFRACTIONf_chiral_restr0.0544491
X-RAY DIFFRACTIONf_plane_restr0.0066601
X-RAY DIFFRACTIONf_dihedral_angle_d4.44252009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.670.41971350.44116799X-RAY DIFFRACTION97.97
1.67-1.760.33711410.33576895X-RAY DIFFRACTION99.46
1.76-1.870.29331350.27156948X-RAY DIFFRACTION99.84
1.87-2.020.33641280.30296772X-RAY DIFFRACTION97.46
2.02-2.220.28311450.2426943X-RAY DIFFRACTION99.45
2.22-2.540.29181340.2426939X-RAY DIFFRACTION98.7
2.54-3.20.23441370.21087079X-RAY DIFFRACTION99.83
3.2-34.250.20261460.16077331X-RAY DIFFRACTION99.84

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