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- PDB-5ik1: Open state of P450cam after soaking in camphor -

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Open data


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Basic information

Entry
Database: PDB / ID: 5ik1
TitleOpen state of P450cam after soaking in camphor
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / conformational state / structural change / crystal contact
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 / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsMahomed, M. / Goodin, D.B. / Lee, Y.-T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM41049 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Effector Roles of Putidaredoxin on Cytochrome P450cam Conformational States.
Authors: Liou, S.H. / Mahomed, M. / Lee, Y.T. / Goodin, D.B.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)46,6034
Polymers45,6821
Non-polymers9213
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-10 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.540, 73.800, 90.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 45681.934 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Bis-Tris 10-22 % PEG 8000 200 mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→57.128 Å / Num. all: 66465 / Num. obs: 66465 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.07 / Rsym value: 0.062 / Net I/av σ(I): 5.688 / Net I/σ(I): 13.4 / Num. measured all: 301754
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.53-1.614.50.4261.81100
1.61-1.714.60.2682.91100
1.71-1.834.60.1664.71100
1.83-1.984.60.1066.81100
1.98-2.164.60.0699.81100
2.16-2.424.60.04713.8199.8
2.42-2.794.50.04314.7199.5
2.79-3.424.30.0618.8199.2
3.42-4.844.30.05211.2199.4
4.84-34.1554.50.05111.2194.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.81 Å34.16 Å
Translation1.81 Å34.16 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
MOLREP10.2.35phasing
REFMACrefinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L62

3l62


Resolution: 1.53→34.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.221 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0724 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.075
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 3369 5.1 %RANDOM
Rwork0.1795 ---
obs0.1808 63035 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 76.2 Å2 / Biso mean: 22.638 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.53→34.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3111 0 65 279 3455
Biso mean--26.11 35.68 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0223297
X-RAY DIFFRACTIONr_angle_refined_deg2.7332.0094507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53423.974156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5715541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.961525
X-RAY DIFFRACTIONr_chiral_restr0.1860.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212562
X-RAY DIFFRACTIONr_mcbond_it1.6081.52004
X-RAY DIFFRACTIONr_mcangle_it2.58823252
X-RAY DIFFRACTIONr_scbond_it3.79431293
X-RAY DIFFRACTIONr_scangle_it5.8574.51253
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 248 -
Rwork0.31 4625 -
all-4873 -
obs--99.96 %

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