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- PDB-1j51: CRYSTAL STRUCTURE OF CYTOCHROME P450CAM MUTANT (F87W/Y96F/V247L/C... -

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Basic information

Entry
Database: PDB / ID: 1j51
TitleCRYSTAL STRUCTURE OF CYTOCHROME P450CAM MUTANT (F87W/Y96F/V247L/C334A) WITH 1,3,5-TRICHLOROBENZENE
ComponentsCYTOCHROME P450CAM
KeywordsOXIDOREDUCTASE / CYTOCHROME P450-CAM
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
PROTOPORPHYRIN IX CONTAINING FE / : / 1,3,5-TRICHLORO-BENZENE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsChen, X. / Christopher, A. / Jones, J. / Guo, Q. / Xu, F. / Cao, R. / Wong, L.L. / Rao, Z.
CitationJournal: J.BIOL.CHEM. / Year: 2002
Title: Crystal structure of the F87W/Y96F/V247L mutant of cytochrome P-450cam with 1,3,5-trichlorobenzene bound and further protein engineering for the oxidation of pentachlorobenzene and hexachlorobenzene
Authors: Chen, X. / Christopher, A. / Jones, J.P. / Bell, S.G. / Guo, Q. / Xu, F. / Rao, Z. / Wong, L.L.
History
DepositionJan 5, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / citation_author / refine
Item: _audit_author.name / _citation_author.name / _refine.ls_d_res_low
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / refine_hist / 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 / _refine_hist.d_res_low / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450CAM
B: CYTOCHROME P450CAM
C: CYTOCHROME P450CAM
D: CYTOCHROME P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,54215
Polymers186,3764
Non-polymers3,16711
Water7,728429
1
A: CYTOCHROME P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4314
Polymers46,5941
Non-polymers8373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4314
Polymers46,5941
Non-polymers8373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CYTOCHROME P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4314
Polymers46,5941
Non-polymers8373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CYTOCHROME P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2493
Polymers46,5941
Non-polymers6562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.87, 62.44, 95.52
Angle α, β, γ (deg.)89.98, 90.30, 90.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CYTOCHROME P450CAM / CAMPHOR 5-MONOOXYGENASE


Mass: 46593.879 Da / Num. of mol.: 4 / Mutation: F87W/Y96F/V247L/C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PCHX / Production host: Escherichia coli (E. coli) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-TCZ / 1,3,5-TRICHLORO-BENZENE


Mass: 181.447 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H3Cl3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: PEG8000, sodium acetate, sodium cacodylate, pH 6.5, EVAPORATION, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMcacodylate1reservoirpH6.5
2200 mM1reservoirKCl
38 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 26, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 286421 / Num. obs: 285817 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.354 / Num. unique all: 7110 / % possible all: 90.1
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 74970 / % possible obs: 95.8 % / Num. measured all: 285817
Reflection shell
*PLUS
% possible obs: 90.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNS1phasing
RefinementResolution: 2.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflection
Rfree0.258 6257 2.2 %
Rwork0.186 --
all-286421 -
obs-285817 99.8 %
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12836 0 203 429 13468
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.74
X-RAY DIFFRACTIONc_angle_deg1.74
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0013

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