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- PDB-4c9n: Structure of camphor and hydroxycamphor bound D259N mutant of CYP101D1 -

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Basic information

Entry
Database: PDB / ID: 4c9n
TitleStructure of camphor and hydroxycamphor bound D259N mutant of 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: 2.2 Å
AuthorsBatabyal, D. / L Poulos, T.
CitationJournal: Biochemistry / Year: 2013
Title: Crystal Structures and Functional Characterization of Wild Type and Active Sites Mutants of Cyp101D1.
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 / 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 / _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)96,6409
Polymers94,6742
Non-polymers1,9667
Water8,719484
1
A: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3665
Polymers47,3371
Non-polymers1,0294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2744
Polymers47,3371
Non-polymers9373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.506, 151.506, 196.391
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME P450 / CYP101D1


Mass: 47336.988 Da / Num. of mol.: 2 / Mutation: YES
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

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Non-polymers , 5 types, 491 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-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical ChemComp-CAH / 5-EXO-HYDROXYCAMPHOR


Mass: 168.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 3.44 Å3/Da / Density % sol: 64.21 % / Description: NONE
Crystal growpH: 8.2 / Details: 100 MM 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: Jun 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.59 Å / Num. obs: 67852 / % possible obs: 100 % / Observed criterion σ(I): 3.4 / Redundancy: 14.5 % / Biso Wilson estimate: 26.57 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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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

3lxi


Resolution: 2.2→49.531 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 2000 3 %
Rwork0.1768 --
obs0.1778 67782 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6471 0 138 484 7093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086813
X-RAY DIFFRACTIONf_angle_d1.1539310
X-RAY DIFFRACTIONf_dihedral_angle_d14.8012533
X-RAY DIFFRACTIONf_chiral_restr0.0781003
X-RAY DIFFRACTIONf_plane_restr0.0051211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.29011400.21914604X-RAY DIFFRACTION100
2.255-2.3160.20571410.20814612X-RAY DIFFRACTION100
2.316-2.38420.26241400.19574612X-RAY DIFFRACTION100
2.3842-2.46110.22291410.18744643X-RAY DIFFRACTION100
2.4611-2.54910.26781400.19194627X-RAY DIFFRACTION100
2.5491-2.65110.24891420.18784650X-RAY DIFFRACTION100
2.6511-2.77180.24321410.17954637X-RAY DIFFRACTION100
2.7718-2.91790.2291430.1874699X-RAY DIFFRACTION100
2.9179-3.10070.2141410.17654667X-RAY DIFFRACTION100
3.1007-3.340.20981430.17644682X-RAY DIFFRACTION100
3.34-3.67610.19451430.16294708X-RAY DIFFRACTION100
3.6761-4.20780.17491450.15674774X-RAY DIFFRACTION100
4.2078-5.30040.16911460.15054803X-RAY DIFFRACTION100
5.3004-49.54380.19891540.19225064X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4357-1.1453-0.72141.30240.06341.6712-0.08290.096-0.1197-0.05590.08470.03680.12710.0265-0.02170.1247-0.0349-0.01020.1965-0.05080.147433.00126.57322.8158
20.6017-0.3582-0.00661.4851-0.04930.4142-0.07420.10480.1745-0.10660.075-0.1954-0.10550.1621-0.00270.1428-0.0571-0.0090.2887-0.03950.213836.772727.39244.907
31.38940.2777-0.38471.13430.23171.1628-0.05050.220.0204-0.21380.04860.2452-0.1113-0.227-0.01270.21430.0166-0.0870.2450.03830.188511.278330.52793.2193
41.6361-0.2566-0.06084.36730.5792.1128-0.02440.20910.2571-0.26530.1095-0.2043-0.22050.1494-0.09450.2241-0.0795-0.02450.28410.04430.211627.559438.6111-4.8692
52.72170.63390.06254.02840.00451.8752-0.1459-0.0601-0.07360.11850.16350.2601-0.0136-0.1085-0.01560.08470.0592-0.02530.21970.02140.177711.120219.243915.6104
62.0988-0.0504-0.25131.1187-0.15230.826-0.1109-0.2565-0.01030.12420.1404-0.0505-0.01250.1455-0.04220.12370.0158-0.03260.2503-0.02350.116530.175319.448514.8008
72.0390.014-0.5932.50650.91312.24-0.084-0.0785-0.24190.0855-0.02340.43090.0088-0.34220.07790.11310.0218-0.0530.24050.0370.20138.122620.534210.5929
82.1928-1.470.1492.9165-0.01350.8544-0.0933-0.49620.04970.36760.18040.14090.11390.1359-0.07550.16470.06270.02960.41780.00330.173137.099415.41142.8358
91.7737-0.2057-0.43910.76640.00660.11760.07050.16020.3731-0.1635-0.1554-0.2353-0.00770.43170.03210.17970.07230.01260.51020.05010.288551.40921.765928.7878
100.7134-0.1751-0.16640.53930.06560.3428-0.058-0.27880.02390.1795-0.1853-0.3810.13360.515-0.01770.23370.22860.00380.82010.12630.441665.47146.925337.7414
111.6406-0.34640.07060.44490.05970.7159-0.00080.0439-0.0516-0.1314-0.0973-0.30570.25420.52990.05950.25640.18610.04490.53890.07730.288258.44116.481528.9786
121.5789-0.431-0.07792.571-0.14040.95080.03710.1699-0.0253-0.18-0.10310.09030.14620.15640.06590.15450.0918-0.02450.32840.00350.158841.413912.456227.7482
131.0411-0.4498-0.23160.91020.17960.8175-0.0169-0.053-0.542-0.0294-0.12-0.01930.48740.3137-0.02150.36220.42590.07660.56150.13210.464255.7719-6.824137.1228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 10 THROUGH 63 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 64 THROUGH 122 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 123 THROUGH 193 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 194 THROUGH 258 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 259 THROUGH 285 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 286 THROUGH 367 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 368 THROUGH 417 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 11 THROUGH 63 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 64 THROUGH 122 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 123 THROUGH 219 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 220 THROUGH 308 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 309 THROUGH 367 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 368 THROUGH 417 )

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