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- PDB-4l4g: Structure of cyanide and camphor bound P450cam mutant L358P/K178G -

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Basic information

Entry
Database: PDB / ID: 4l4g
TitleStructure of cyanide and camphor bound P450cam mutant L358P/K178G
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 / 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: 1.55 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)47,5127
Polymers46,6001
Non-polymers9126
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.072, 58.790, 57.072
Angle α, β, γ (deg.)90.00, 105.02, 90.00
Int Tables number4
Space group name H-MP1211

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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: 46599.840 Da / Num. of mol.: 1 / Mutation: C334A, K178G, L358P
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, 452 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.: 3 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 1.98 Å3/Da / Density % sol: 38.02 %
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: Jul 6, 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: 1.55→50 Å / Num. obs: 53044 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 5.6
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceIcedata 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: 1.55→35.876 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 2652 5.01 %
Rwork0.1725 --
obs0.1745 52974 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→35.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 59 446 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083342
X-RAY DIFFRACTIONf_angle_d1.2384554
X-RAY DIFFRACTIONf_dihedral_angle_d14.5111245
X-RAY DIFFRACTIONf_chiral_restr0.086488
X-RAY DIFFRACTIONf_plane_restr0.006602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57820.27841420.24692633X-RAY DIFFRACTION100
1.5782-1.60860.24451390.22212608X-RAY DIFFRACTION100
1.6086-1.64140.26131380.20752668X-RAY DIFFRACTION100
1.6414-1.67710.27381400.20612647X-RAY DIFFRACTION100
1.6771-1.71610.24831380.2022614X-RAY DIFFRACTION100
1.7161-1.7590.22471360.19582610X-RAY DIFFRACTION100
1.759-1.80660.26911380.19952640X-RAY DIFFRACTION100
1.8066-1.85970.22951400.19012684X-RAY DIFFRACTION100
1.8597-1.91970.34231380.25162609X-RAY DIFFRACTION99
1.9197-1.98840.24591390.20392634X-RAY DIFFRACTION100
1.9884-2.0680.25751390.19912638X-RAY DIFFRACTION100
2.068-2.16210.22531390.18252660X-RAY DIFFRACTION100
2.1621-2.2760.2431440.19112645X-RAY DIFFRACTION99
2.276-2.41860.21651410.16552632X-RAY DIFFRACTION100
2.4186-2.60530.20441370.1662661X-RAY DIFFRACTION100
2.6053-2.86740.22331380.16632647X-RAY DIFFRACTION100
2.8674-3.2820.18671390.15842690X-RAY DIFFRACTION100
3.282-4.13410.1681410.1392680X-RAY DIFFRACTION100
4.1341-35.88530.1471460.13642722X-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)
11.9109-0.0133-0.56670.9520.05681.2222-0.0235-0.21020.00720.07220.0494-0.219-0.04050.445-0.00090.1076-0.0092-0.01380.2336-0.00010.182625.110110.19610.3845
20.7989-0.0714-0.25760.44520.20561.2766-0.002-0.0135-0.07590.0415-0.01950.02760.0688-0.05110.02710.1274-0.00750.00040.0940.00210.1258-1.46954.34199.3754
30.7472-0.0254-0.5460.67370.08371.67820.01-0.10720.0380.04540.0044-0.0358-0.08050.1195-0.01170.0992-0.0055-0.00290.0780.00250.10136.872815.110113.8361
41.19130.9391-1.7310.7567-1.18494.7765-0.1136-0.3653-0.17640.1235-0.07840.01350.18660.32160.12760.12560.01-0.00960.16680.03290.1222.73345.352531.8569
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 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 377 )
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 414 )

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