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- PDB-6wgw: CYP101D1 D259E Hydroxycamphor bound -

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Basic information

Entry
Database: PDB / ID: 6wgw
TitleCYP101D1 D259E Hydroxycamphor bound
ComponentsCytochrome P450 101D1
KeywordsOXIDOREDUCTASE / P450cam / D251E / camphor / PdX / PdR
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 / membrane
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5-EXO-HYDROXYCAMPHOR / CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 6, 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.pdbx_ptnr2_label_alt_id / _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: 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 101D1
B: Cytochrome P450 101D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,32411
Polymers98,2182
Non-polymers2,1069
Water16,250902
1
A: Cytochrome P450 101D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2787
Polymers49,1091
Non-polymers1,1696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 101D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0464
Polymers49,1091
Non-polymers9373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.426, 152.426, 196.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11B-980-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450 101D1 / CYP101D1


Mass: 49108.867 Da / Num. of mol.: 2 / Mutation: D259E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Gene: Saro_0514 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q2GB12

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Non-polymers , 5 types, 911 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAH / 5-EXO-HYDROXYCAMPHOR


Mass: 168.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 1.6 M ammonium sulfate; 0.1 M Tris

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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: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→48.36 Å / Num. obs: 278914 / % possible obs: 99.99 % / Redundancy: 2 % / Biso Wilson estimate: 26.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.46
Reflection shellResolution: 1.73→1.792 Å / Num. unique obs: 13748 / CC1/2: 0.453

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C9K

4c9k


Resolution: 1.73→48.36 Å / SU ML: 0.2677 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6595
RfactorNum. reflection% reflection
Rfree0.2124 2000 1.43 %
Rwork0.1889 --
obs0.1893 139452 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.38 Å2
Refinement stepCycle: LAST / Resolution: 1.73→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 20 902 7516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746814
X-RAY DIFFRACTIONf_angle_d0.97149308
X-RAY DIFFRACTIONf_chiral_restr0.05471001
X-RAY DIFFRACTIONf_plane_restr0.00571209
X-RAY DIFFRACTIONf_dihedral_angle_d8.6497925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.39641410.38489687X-RAY DIFFRACTION99.98
1.77-1.820.40761400.33659672X-RAY DIFFRACTION100
1.82-1.870.3021420.29319681X-RAY DIFFRACTION100
1.87-1.940.27751410.24779722X-RAY DIFFRACTION100
1.94-20.26531410.21739735X-RAY DIFFRACTION100
2-2.080.25161420.20829711X-RAY DIFFRACTION100
2.08-2.180.25391420.20489753X-RAY DIFFRACTION99.99
2.18-2.290.21691410.19989720X-RAY DIFFRACTION100
2.29-2.440.19921420.19079788X-RAY DIFFRACTION99.99
2.44-2.630.22731440.18879814X-RAY DIFFRACTION100
2.63-2.890.22531430.1859845X-RAY DIFFRACTION100
2.89-3.310.19651430.1799897X-RAY DIFFRACTION100
3.31-4.170.161460.155810003X-RAY DIFFRACTION100
4.17-48.360.18351520.162410424X-RAY DIFFRACTION99.97

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