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- PDB-4c9k: Structure of Camphor and Hydroxycamphor bound wild type CYP101D1 -

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Basic information

Entry
Database: PDB / ID: 4c9k
TitleStructure of Camphor and Hydroxycamphor bound wild type CYP101D1
ComponentsCYTOCHROME P450
KeywordsOXIDOREDUCTASE / MONO-OXYGENASE
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: 2.18 Å
AuthorsBatabyal, D. / L Poulos, T.
CitationJournal: Biochemistry / Year: 2013
Title: Crystal Structures and Functional Characterization of Wild-Type Cyp101D1 and its Active Site Mutants.
Authors: Batabyal, D. / Poulos, T.L.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450
B: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5508
Polymers94,6762
Non-polymers1,8746
Water9,782543
1
A: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2754
Polymers47,3381
Non-polymers9373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2754
Polymers47,3381
Non-polymers9373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.318, 151.318, 196.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein CYTOCHROME P450 / CYP101D1


Mass: 47337.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NOVOSPHINGOBIUM AROMATICIVORANS (bacteria)
Strain: DSM12444 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GB12
#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
#4: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 3.42 Å3/Da / Density % sol: 64.07 % / Description: NONE
Crystal growpH: 8.2 / Details: 100MM TRIS PH 8.2, 1.6M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50.2 Å / Num. obs: 69832 / % possible obs: 99.9 % / Observed criterion σ(I): 7 / Redundancy: 14.2 % / Biso Wilson estimate: 30.87 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.4
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LXI
Resolution: 2.18→49.53 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 3459 5 %
Rwork0.1753 --
obs0.1775 68585 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6471 0 132 543 7146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076800
X-RAY DIFFRACTIONf_angle_d1.1559292
X-RAY DIFFRACTIONf_dihedral_angle_d14.3022528
X-RAY DIFFRACTIONf_chiral_restr0.0791001
X-RAY DIFFRACTIONf_plane_restr0.0041209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.20990.22691290.18412559X-RAY DIFFRACTION98
2.2099-2.24150.23041460.17972559X-RAY DIFFRACTION100
2.2415-2.27490.22191370.18522585X-RAY DIFFRACTION100
2.2749-2.31050.23421520.17772586X-RAY DIFFRACTION100
2.3105-2.34830.21681220.17552589X-RAY DIFFRACTION100
2.3483-2.38880.24531500.1752584X-RAY DIFFRACTION100
2.3888-2.43230.22991440.17462575X-RAY DIFFRACTION100
2.4323-2.4790.22351460.17442605X-RAY DIFFRACTION100
2.479-2.52960.21851270.18182588X-RAY DIFFRACTION100
2.5296-2.58460.22141330.18052610X-RAY DIFFRACTION100
2.5846-2.64480.25591540.18252575X-RAY DIFFRACTION100
2.6448-2.71090.21081310.17962570X-RAY DIFFRACTION98
2.7109-2.78420.24581300.19822509X-RAY DIFFRACTION96
2.7842-2.86610.30591500.20342516X-RAY DIFFRACTION97
2.8661-2.95860.25111350.19922548X-RAY DIFFRACTION97
2.9586-3.06430.26211360.19652537X-RAY DIFFRACTION97
3.0643-3.1870.2221430.19542569X-RAY DIFFRACTION98
3.187-3.3320.2451420.18492566X-RAY DIFFRACTION98
3.332-3.50770.22611370.17122602X-RAY DIFFRACTION98
3.5077-3.72740.23061330.16342603X-RAY DIFFRACTION98
3.7274-4.0150.19351440.16082631X-RAY DIFFRACTION99
4.015-4.41890.1781340.14612683X-RAY DIFFRACTION100
4.4189-5.05770.16331230.14662724X-RAY DIFFRACTION100
5.0577-6.37010.2021430.18742733X-RAY DIFFRACTION100
6.3701-49.54320.20031380.18372920X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9977-0.8986-0.08481.65520.05510.7145-0.00290.05580.0659-0.15430.0264-0.1302-0.0590.1023-0.02560.1375-0.0286-0.01320.2373-0.02610.141734.896617.51873.9519
21.38280.3161-0.17920.94180.45281.3327-0.04160.05030.0419-0.2890.03710.283-0.1262-0.13930.00180.25410.0298-0.0960.21940.0220.202511.196930.43983.2587
31.61250.35020.27733.68110.15062.159-0.09160.1920.3018-0.23170.1556-0.1511-0.35370.2898-0.08160.2954-0.0529-0.02030.25030.03890.207227.4339.0408-5.4925
41.6064-0.2587-0.29581.00120.02571.0073-0.1023-0.155-0.03310.03810.07920.057-0.08690.0060.01560.14560.0023-0.0370.1931-0.01010.122825.314821.255913.0435
51.6818-0.2735-0.23182.05290.59222.2364-0.0559-0.0611-0.22780.0241-0.04010.4035-0.0034-0.32550.08080.11710.0138-0.05260.22110.03450.21658.085620.450510.6044
61.8915-1.0077-0.02481.80350.15161.0448-0.0243-0.30750.10060.10840.07980.11020.01790.0309-0.05780.1120.02150.00320.3065-0.02570.164839.267517.092338.284
71.931-0.5472-0.19061.7608-0.28460.5769-0.02130.05560.2012-0.1091-0.0484-0.2905-0.01840.10230.07130.12980.01720.01130.35070.01710.263562.613311.132227.276
81.05921.0732-0.36821.4053-0.02311.1148-0.0296-0.422-0.30110.0968-0.0962-0.34150.2250.22320.12780.15490.0780.0170.32490.05820.320265.6254-2.465337.8385
93.3013-0.2278-0.34641.43750.1032.4252-0.0117-0.39240.32530.0812-0.0342-0.3262-0.16490.14720.04360.1667-0.0043-0.06870.3598-0.00740.365166.594218.52235.9539
102.1307-0.88820.0542.5905-0.21170.93260.00720.0788-0.2318-0.1776-0.01270.12020.1017-0.04840.01050.1090.00630.00020.24060.01040.164145.32984.996628.8456
112.128-0.6496-0.19672.23140.70782.1859-0.1132-0.1254-0.5820.22140.05170.06110.42820.09740.07090.15620.05660.01760.26820.06270.345855.4799-6.94737.1029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 10 THROUGH 122 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 123 THROUGH 193 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 194 THROUGH 242 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 243 THROUGH 367 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 368 THROUGH 417 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 11 THROUGH 91 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 92 THROUGH 145 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 146 THROUGH 172 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 173 THROUGH 259 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 260 THROUGH 367 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 368 THROUGH 417 )

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