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- PDB-4l4b: Structure of L358A/K178G/D182N mutant of P450cam bound to camphor -

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Basic information

Entry
Database: PDB / ID: 4l4b
TitleStructure of L358A/K178G/D182N 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: 2.099 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_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_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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4205
Polymers46,5731
Non-polymers8474
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.503, 103.587, 105.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46572.816 Da / Num. of mol.: 1 / Mutation: C334A, K178G,L358A,D182N
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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#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


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
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: Feb 29, 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: 2.099→50 Å / Num. obs: 22278 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 34
Reflection shellResolution: 2.099→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 12 / % possible all: 80

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPP

2cpp


Resolution: 2.099→34.508 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 1145 5.15 %
Rwork0.1763 --
obs0.1794 22224 91.42 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→34.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 56 293 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073349
X-RAY DIFFRACTIONf_angle_d1.1554573
X-RAY DIFFRACTIONf_dihedral_angle_d15.7491246
X-RAY DIFFRACTIONf_chiral_restr0.075489
X-RAY DIFFRACTIONf_plane_restr0.006603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0989-2.19440.22661360.17252113X-RAY DIFFRACTION75
2.1944-2.31010.24781150.17072272X-RAY DIFFRACTION80
2.3101-2.45470.25121090.17772398X-RAY DIFFRACTION84
2.4547-2.64420.25481300.18522690X-RAY DIFFRACTION94
2.6442-2.91020.27351640.20192806X-RAY DIFFRACTION99
2.9102-3.3310.26191660.19872890X-RAY DIFFRACTION100
3.331-4.19550.23131580.16822872X-RAY DIFFRACTION99
4.1955-34.51310.19531670.15643038X-RAY DIFFRACTION99
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)
10.9215-0.2377-0.2081.791.16672.0735-0.019-0.09970.105-0.0104-0.04230.2969-0.2522-0.11390.06320.10180.01340.0370.16070.0010.15916.78331.5173-22.2492
20.7997-0.059-0.22852.4260.52660.3135-0.1502-0.2402-0.07050.75550.19110.00290.05140.1132-0.02490.27350.04520.0020.22820.0180.137815.5629-9.7463-12.4016
30.9198-0.5381-0.3132.05230.29630.8807-0.1618-0.1762-0.29670.26220.09890.35860.16940.00960.03160.1564-0.00490.03530.16840.04980.237511.599-28.818-23.7998
40.6348-0.29-0.09312.05810.95271.3854-0.02570.0049-0.0323-0.10860.1094-0.0656-0.04840.1297-0.08070.0864-0.0103-0.00290.1278-0.0060.100119.7896-12.7657-31.4496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 266 )
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 414 )

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