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- PDB-4l4c: Structure of L358P/K178G mutant of P450cam bound to camphor -

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Basic information

Entry
Database: PDB / ID: 4l4c
TitleStructure of L358P/K178G mutant of P450cam bound to camphor
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / mono-oxygenase / cytochrome P450
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBatabyal, D. / Li, H. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2013
Title: Synergistic Effects of Mutations in Cytochrome P450cam Designed To Mimic CYP101D1.
Authors: Batabyal, D. / Li, H. / Poulos, T.L.
History
DepositionJun 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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 / _struct_ref_seq_dif.details / _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: Camphor 5-monooxygenase
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8549
Polymers93,2002
Non-polymers1,6557
Water9,800544
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4475
Polymers46,6001
Non-polymers8474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4084
Polymers46,6001
Non-polymers8083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.581, 61.519, 94.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 46599.840 Da / Num. of mol.: 2 / Mutation: C334A, L358P, K178G
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-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
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50 mM Tris, 400 mM potassium chloride, 32% PEG4000, 1.2 mM D-camphor, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2012
RadiationMonochromator: VariMax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37084 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.4 / % possible all: 68

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPP

2cpp


Resolution: 2.2→29.263 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 1846 4.98 %
Rwork0.17 --
obs0.1738 37065 93.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 111 544 7057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086686
X-RAY DIFFRACTIONf_angle_d1.2369128
X-RAY DIFFRACTIONf_dihedral_angle_d16.2222490
X-RAY DIFFRACTIONf_chiral_restr0.081976
X-RAY DIFFRACTIONf_plane_restr0.0051204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.25980.2626840.19771605X-RAY DIFFRACTION56
2.2598-2.32630.32551140.18332330X-RAY DIFFRACTION81
2.3263-2.40130.27241380.17512663X-RAY DIFFRACTION92
2.4013-2.48710.27441300.18562720X-RAY DIFFRACTION93
2.4871-2.58660.28361430.18622720X-RAY DIFFRACTION94
2.5866-2.70430.28751300.19272803X-RAY DIFFRACTION96
2.7043-2.84680.27841450.20822862X-RAY DIFFRACTION99
2.8468-3.02490.29351540.21082873X-RAY DIFFRACTION99
3.0249-3.25820.29221710.18682902X-RAY DIFFRACTION100
3.2582-3.58560.23011660.17382875X-RAY DIFFRACTION100
3.5856-4.10320.20821600.14492917X-RAY DIFFRACTION100
4.1032-5.1650.18341500.12462959X-RAY DIFFRACTION100
5.165-29.26520.17331610.14062990X-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)
11.8992-0.15070.05031.33950.41532.8099-0.05580.22120.0337-0.060.0096-0.086-0.05990.2640.05660.0968-0.0151-0.00040.11060.01870.1289-12.17426.7226-63.0198
21.98120.2015-1.29681.1680.56985.40140.02980.10850.01520.0181-0.06510.2924-0.2231-0.4053-0.01490.1181-0.005-0.02130.08170.00280.1981-32.70928.2616-53.68
37.9185-3.90245.21865.0592-3.09145.2165-0.3024-0.93490.07120.7034-0.07520.3387-0.6426-0.70070.21460.2992-0.06020.02970.3872-0.11490.1786-21.26367.5209-25.613
41.62490.28760.80071.21940.16211.06870.0392-0.1733-0.17720.0794-0.00220.0530.0089-0.1141-0.05640.1238-0.00590.01230.10630.01520.1542-27.8609-0.5922-41.4816
50.75630.0783-0.00350.45820.13211.8902-0.0253-0.03140.11280.082-0.0658-0.0758-0.27810.16420.10040.1591-0.0304-0.02020.0941-0.00280.1595-12.961314.7321-46.575
62.3793-0.08822.35971.0738-0.98034.40640.250.0511-0.12190.2571-0.0301-0.2380.30830.3739-0.20260.1881-0.0115-0.05530.15940.02920.1891-4.98731.0739-33.0307
70.7773-0.3085-0.31861.0857-0.2112.5226-0.1318-0.3063-0.01910.28210.15450.25660.0068-0.5476-0.02960.23730.04170.05020.3730.01070.1679-24.6145-23.703810.3357
81.9069-0.09-1.34290.3892-1.1136.4809-0.0119-0.16940.19290.0817-0.1738-0.2952-0.48180.33770.12520.1976-0.0119-0.03660.13320.01590.2641-1.9145-21.07562.0929
91.0349-0.91431.37240.878-0.9312.75660.17630.0987-0.0179-0.0989-0.0538-0.03020.42870.0972-0.11640.17940.0096-0.00540.1186-0.00360.157-6.7189-32.6462-12.3528
105.495-1.42452.25551.2482-0.65551.19430.0945-0.1323-0.09530.080.0433-0.08620.0064-0.0729-0.08850.1618-0.01460.03550.15950.02370.1146-2.2491-25.4623-5.1342
110.8256-0.0442-0.25220.8606-0.55222.235-0.1265-0.14220.1110.20720.14720.0712-0.3565-0.3758-0.04870.16890.04210.01870.1884-0.02390.1665-22.8703-15.6183-2.1168
121.37280.16831.54790.66990.37493.3007-0.05990.11110.1441-0.0011-0.076-0.0528-0.44480.02910.08170.17150.0079-0.00110.12770.01770.12-14.5084-14.7949-11.4784
132.56070.43911.99481.14651.09322.08160.0049-0.1815-0.0849-0.1817-0.00430.02060.6659-0.6703-0.06040.1922-0.0620.00110.2470.0010.1523-24.9953-28.2027-20.5463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 377 )
6X-RAY DIFFRACTION6chain 'A' and (resid 378 through 414 )
7X-RAY DIFFRACTION7chain 'B' and (resid 10 through 89 )
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 127 )
9X-RAY DIFFRACTION9chain 'B' and (resid 128 through 213 )
10X-RAY DIFFRACTION10chain 'B' and (resid 214 through 265 )
11X-RAY DIFFRACTION11chain 'B' and (resid 266 through 340 )
12X-RAY DIFFRACTION12chain 'B' and (resid 341 through 377 )
13X-RAY DIFFRACTION13chain 'B' and (resid 378 through 414 )

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