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- PDB-6we6: Camphor bound P450cam D251E structure -

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Basic information

Entry
Database: PDB / ID: 6we6
TitleCamphor bound P450cam D251E structure
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
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Camphor 5-monooxygenase
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0208
Polymers93,4042
Non-polymers1,6166
Water4,954275
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5104
Polymers46,7021
Non-polymers8083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5104
Polymers46,7021
Non-polymers8083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.657, 62.204, 224.184
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: 46702.039 Da / Num. of mol.: 2 / Mutation: D251E/C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAM / CAMPHOR / Camphor


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50 mM Tris, 10% PEG 4000, 200 mM potassium chloride, 2 mM D-camphor

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.158→37.36 Å / Num. obs: 87694 / % possible obs: 98.48 % / Redundancy: 2 % / Biso Wilson estimate: 31.48 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.09
Reflection shellResolution: 2.16→2.236 Å / Num. unique obs: 44051 / CC1/2: 0.609 / % possible all: 90.24

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WK7

5wk7


Resolution: 2.16→37.36 Å / SU ML: 0.277 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.8519
RfactorNum. reflection% reflection
Rfree0.2562 3762 4.58 %
Rwork0.2043 --
obs0.2067 82169 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.05 Å2
Refinement stepCycle: LAST / Resolution: 2.16→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 2 275 6793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096690
X-RAY DIFFRACTIONf_angle_d1.06399132
X-RAY DIFFRACTIONf_chiral_restr0.0551980
X-RAY DIFFRACTIONf_plane_restr0.0061202
X-RAY DIFFRACTIONf_dihedral_angle_d8.14794010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.190.31091200.25752264X-RAY DIFFRACTION77.2
2.19-2.220.34721150.27272970X-RAY DIFFRACTION97.2
2.22-2.250.37381350.29272765X-RAY DIFFRACTION95.87
2.25-2.280.43881320.30892923X-RAY DIFFRACTION99
2.28-2.310.2971370.27472952X-RAY DIFFRACTION99.01
2.31-2.350.3011430.2512895X-RAY DIFFRACTION99.41
2.35-2.390.33361590.25462951X-RAY DIFFRACTION99.36
2.39-2.430.29281360.24592947X-RAY DIFFRACTION99.74
2.43-2.470.35241320.26032943X-RAY DIFFRACTION98.59
2.47-2.520.31941270.24482883X-RAY DIFFRACTION97.85
2.52-2.570.27281530.23232963X-RAY DIFFRACTION99.78
2.57-2.630.29051340.21512929X-RAY DIFFRACTION99.77
2.63-2.690.31081180.21962913X-RAY DIFFRACTION99.57
2.69-2.760.23941670.22582955X-RAY DIFFRACTION99.55
2.76-2.830.25831310.21792960X-RAY DIFFRACTION99.68
2.83-2.910.26141480.2232932X-RAY DIFFRACTION99.68
2.91-3.010.3161300.22662939X-RAY DIFFRACTION99.74
3.01-3.110.29391430.22952955X-RAY DIFFRACTION99.61
3.11-3.240.27871550.24982885X-RAY DIFFRACTION99.15
3.24-3.390.28681330.212965X-RAY DIFFRACTION99.42
3.39-3.570.2361510.18422934X-RAY DIFFRACTION99.84
3.57-3.790.22681470.18582906X-RAY DIFFRACTION99.51
3.79-4.080.23921360.17092965X-RAY DIFFRACTION99.49
4.08-4.490.21671440.15642931X-RAY DIFFRACTION99.32
4.49-5.140.19651430.16142913X-RAY DIFFRACTION99.03
5.14-6.470.21491460.18462940X-RAY DIFFRACTION99.42
6.47-37.360.19021470.1572929X-RAY DIFFRACTION99.74

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