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- PDB-4l4e: Structure of cyanide and camphor bound P450cam mutant L358A/K178G -

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Basic information

Entry
Database: PDB / ID: 4l4e
TitleStructure of cyanide and camphor bound P450cam mutant L358A/K178G
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 / CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.261 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 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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)47,4476
Polymers46,5741
Non-polymers8735
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.644, 103.594, 106.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 46573.805 Da / Num. of mol.: 1 / Mutation: C334A, K178G, L358A
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

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Non-polymers , 5 types, 525 molecules

#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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 109438 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 39
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceIcedata 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: 1.261→34.546 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 5465 5 %
Rwork0.1895 --
obs0.1905 109358 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.261→34.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 58 520 3777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083339
X-RAY DIFFRACTIONf_angle_d1.2154549
X-RAY DIFFRACTIONf_dihedral_angle_d15.1911242
X-RAY DIFFRACTIONf_chiral_restr0.082488
X-RAY DIFFRACTIONf_plane_restr0.006601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2605-1.27490.32361470.26663209X-RAY DIFFRACTION93
1.2749-1.28990.29491570.25293444X-RAY DIFFRACTION100
1.2899-1.30560.28751770.24513476X-RAY DIFFRACTION100
1.3056-1.32210.26072020.23493383X-RAY DIFFRACTION100
1.3221-1.33950.23752000.23913413X-RAY DIFFRACTION100
1.3395-1.35790.30991850.23423477X-RAY DIFFRACTION100
1.3579-1.37730.24461610.2243417X-RAY DIFFRACTION100
1.3773-1.39780.22951830.21563436X-RAY DIFFRACTION100
1.3978-1.41970.26551770.21373446X-RAY DIFFRACTION100
1.4197-1.44290.22581820.19983424X-RAY DIFFRACTION100
1.4429-1.46780.21991960.19863479X-RAY DIFFRACTION100
1.4678-1.49450.24231770.19033405X-RAY DIFFRACTION100
1.4945-1.52330.21491910.19433479X-RAY DIFFRACTION100
1.5233-1.55440.19362060.19013376X-RAY DIFFRACTION100
1.5544-1.58820.21481840.18953506X-RAY DIFFRACTION100
1.5882-1.62510.19511710.18343437X-RAY DIFFRACTION100
1.6251-1.66570.20091630.17723502X-RAY DIFFRACTION100
1.6657-1.71080.19211760.18023445X-RAY DIFFRACTION100
1.7108-1.76110.21681820.18833459X-RAY DIFFRACTION100
1.7611-1.8180.19241870.19433495X-RAY DIFFRACTION100
1.818-1.88290.20861760.19333459X-RAY DIFFRACTION100
1.8829-1.95830.18811780.18823485X-RAY DIFFRACTION100
1.9583-2.04740.21481910.1943487X-RAY DIFFRACTION100
2.0474-2.15540.20511930.18493496X-RAY DIFFRACTION100
2.1554-2.29040.23041870.17993487X-RAY DIFFRACTION100
2.2904-2.46720.19841800.18893497X-RAY DIFFRACTION100
2.4672-2.71540.2121880.18963504X-RAY DIFFRACTION100
2.7154-3.10810.22621670.20113567X-RAY DIFFRACTION100
3.1081-3.9150.20342060.18063548X-RAY DIFFRACTION99
3.915-34.55940.19081950.17263655X-RAY DIFFRACTION97
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)
10.40680.15270.17111.85760.53720.8562-0.03530.06350.0275-0.19390.04890.0697-0.0323-0.0202-0.01150.0596-0.001-0.00870.10930.0160.098413.619413.824421.5017
20.8588-0.32270.66722.0415-0.45332.1166-0.11080.13230.1946-0.2652-0.00180.2044-0.2331-0.14330.08850.1499-0.0014-0.02340.15280.0170.21779.176527.473918.1558
30.52660.04960.02031.64360.84971.6637-0.0172-0.04530.01680.12150.0491-0.03970.06560.0336-0.03270.05940.0019-0.00120.0750.00470.084119.799312.846831.4792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 170 )
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 266 )
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 414 )

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