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- PDB-4l4f: Structure of cyanide and camphor bound P450cam mutant L358A/K178G... -

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Basic information

Entry
Database: PDB / ID: 4l4f
TitleStructure of cyanide and camphor bound P450cam mutant L358A/K178G/D182N
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / mono-oxygenase / cytochrome P450 / cyanide complex
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol 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: 1.294 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)47,4466
Polymers46,5731
Non-polymers8735
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.565, 103.413, 106.043
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: 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

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Non-polymers , 5 types, 514 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.: 509 / 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: 42.85 %
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: 1.294→50 Å / Num. obs: 95488 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 35
Reflection shellResolution: 1.294→1.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 94

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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: 1.294→33.448 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 4770 5 %
Rwork0.1949 --
obs0.1959 95394 94.26 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.294→33.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 58 509 3766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083339
X-RAY DIFFRACTIONf_angle_d1.1964549
X-RAY DIFFRACTIONf_dihedral_angle_d14.8921242
X-RAY DIFFRACTIONf_chiral_restr0.083488
X-RAY DIFFRACTIONf_plane_restr0.006601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2941-1.30880.32271360.31122585X-RAY DIFFRACTION81
1.3088-1.32420.30541570.28692921X-RAY DIFFRACTION94
1.3242-1.34030.30681380.27072968X-RAY DIFFRACTION94
1.3403-1.35730.2531610.26472992X-RAY DIFFRACTION93
1.3573-1.37510.28191460.24832929X-RAY DIFFRACTION93
1.3751-1.3940.28851570.23762952X-RAY DIFFRACTION94
1.394-1.41390.24631550.23652975X-RAY DIFFRACTION93
1.4139-1.4350.23621590.22282924X-RAY DIFFRACTION93
1.435-1.45740.22881510.21472957X-RAY DIFFRACTION92
1.4574-1.48130.25551490.21442913X-RAY DIFFRACTION92
1.4813-1.50690.23171480.21832942X-RAY DIFFRACTION93
1.5069-1.53430.25221400.21172948X-RAY DIFFRACTION92
1.5343-1.56380.23731590.20352936X-RAY DIFFRACTION93
1.5638-1.59570.21471700.212984X-RAY DIFFRACTION94
1.5957-1.63040.23011480.19753019X-RAY DIFFRACTION94
1.6304-1.66830.24511580.1993064X-RAY DIFFRACTION95
1.6683-1.710.22571950.19662999X-RAY DIFFRACTION96
1.71-1.75630.24371570.19883087X-RAY DIFFRACTION95
1.7563-1.80790.23071570.19793061X-RAY DIFFRACTION96
1.8079-1.86630.23711420.19773064X-RAY DIFFRACTION96
1.8663-1.9330.19651850.19433073X-RAY DIFFRACTION96
1.933-2.01040.21651650.19853071X-RAY DIFFRACTION96
2.0104-2.10180.22131770.18613035X-RAY DIFFRACTION96
2.1018-2.21260.20081810.1883083X-RAY DIFFRACTION96
2.2126-2.35120.18391460.17953127X-RAY DIFFRACTION96
2.3512-2.53270.21731680.18753136X-RAY DIFFRACTION97
2.5327-2.78750.20711710.19693240X-RAY DIFFRACTION99
2.7875-3.19060.21441730.20343231X-RAY DIFFRACTION99
3.1906-4.01870.21211790.18263214X-RAY DIFFRACTION97
4.0187-33.45890.18541420.17723194X-RAY DIFFRACTION91
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)
10.82330.17020.19942.11930.12780.8596-0.02650.14950.0064-0.33730.06710.09420.0391-0.0064-0.03070.1139-0.0085-0.01320.124-0.00270.091712.59415.986515.6223
20.62470.08720.32011.68690.28121.6389-0.09380.10560.1676-0.22430.01290.1692-0.1523-0.11430.05680.10640.0116-0.00460.13410.02290.178511.41528.699123.8015
30.48330.0206-0.0011.64250.76781.4222-0.0133-0.02040.01750.07250.0537-0.05880.05280.0226-0.03810.0602-0.0005-0.00010.08380.00230.089719.693112.809331.4432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 120 )
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 266 )
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 414 )

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