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- PDB-2fe6: P450CAM from Pseudomonas putida reconstituted with manganic proto... -

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Basic information

Entry
Database: PDB / ID: 2fe6
TitleP450CAM from Pseudomonas putida reconstituted with manganic protoporphyrin IX
ComponentsCytochrome P450-cam
KeywordsOXIDOREDUCTASE / MONO-OXYGENASE / HEME / Manganic / Substrate-Free
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 MN / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
Authorsvon Koenig, K. / Makris, T.M. / Sligar, S.G. / Schlichting, I.
CitationJournal: J.Inorg.Biochem. / Year: 2006
Title: The status of high-valent metal oxo complexes in the P450 cytochromes.
Authors: Makris, T.M. / Koenig, K. / Schlichting, I. / Sligar, S.G.
History
DepositionDec 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 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 / 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 / _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: Cytochrome P450-cam
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2043
Polymers47,5491
Non-polymers6552
Water7,746430
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.390, 64.390, 252.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 47548.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): AW804 (DE3) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MNR / PROTOPORPHYRIN IX CONTAINING MN


Mass: 615.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32MnN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 7.5 MG/ML P450, 50 MM TRIS, 125 MM KCL, 13.5-15% PEG8000, 50 MM DTE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 29, 2005 / Details: Si(111) monochromator, dynamically bendable mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.4→18 Å / Num. obs: 84598 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19 Å2 / Rsym value: 0.086 / Net I/σ(I): 7.01
Reflection shellResolution: 1.4→1.5 Å / Mean I/σ(I) obs: 2.38 / Num. unique all: 30433 / Num. unique obs: 18162 / Rsym value: 0.24 / % possible all: 93.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
MAR345data collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1yrd

1yrd


Resolution: 1.5→18 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: initial parameters for Mn porphyrin IX from: Suslick, K.S. et al. (1991), Inorg. Chem. 30, 2311-17.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 4230 4.9 %throughout
Rwork0.227 ---
all0.236 84586 --
obs0.236 84586 97.9 %-
Solvent computationBsol: 52.904 Å2
Displacement parametersBiso mean: 16.327 Å2
Baniso -1Baniso -2Baniso -3
1-2.148 Å20 Å20 Å2
2--2.148 Å20 Å2
3----4.296 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 44 430 3682
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.34
LS refinement shellResolution: 1.5→1.6 Å / Num. reflection obs: 26508
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2p450_mn_heme_weak_3+.parp450_mn_heme.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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