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- PDB-2qbo: Crystal structure of the P450cam G248V mutant in the cyanide boun... -

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Basic information

Entry
Database: PDB / ID: 2qbo
TitleCrystal structure of the P450cam G248V mutant in the cyanide bound state
ComponentsCytochrome P450-cam
KeywordsOXIDOREDUCTASE / CYP101 / mutant / conserved active site residue / cyanide complex / Gly248 / heme geometry
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 / FOURIER SYNTHESIS / Resolution: 1.9 Å
Authorsvon Koenig, K. / Makris, T.M. / Sligar, S.D. / Schlichting, I.
CitationJournal: Biochemistry / Year: 2007
Title: Alteration of P450 Distal Pocket Solvent Leads to Impaired Proton Delivery and Changes in Heme Geometry.
Authors: Makris, T.M. / Koenig, K.V. / Schlichting, I. / Sligar, S.G.
History
DepositionJun 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450-cam
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4255
Polymers47,5911
Non-polymers8344
Water9,368520
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.680, 63.680, 241.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-878-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 47591.023 Da / Num. of mol.: 1 / Mutation: G248V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase

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Non-polymers , 5 types, 524 molecules

#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1 UL OF 15 MG/ML P450 IN 50 MM Potassium phosphate, 250 MM KCL WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (100 mM Tris, 250 mM KCl, 27-30% PEG 8000, 100 MM DTE), pH 7.4, VAPOR ...Details: 1 UL OF 15 MG/ML P450 IN 50 MM Potassium phosphate, 250 MM KCL WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (100 mM Tris, 250 mM KCl, 27-30% PEG 8000, 100 MM DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.006 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2005 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 39886 / Num. obs: 39886 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rsym value: 0.049 / Net I/σ(I): 15
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 5399 / Rsym value: 0.334 / % possible all: 96

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
MAR345softwaredata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1yrc

1yrc


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1995 4.9 %random
Rwork0.201 ---
all-39886 --
obs-39886 98.8 %-
Solvent computationBsol: 39.019 Å2
Displacement parametersBiso mean: 33.067 Å2
Baniso -1Baniso -2Baniso -3
1-4.288 Å20 Å20 Å2
2--4.288 Å20 Å2
3----8.575 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 57 520 3802
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.269
X-RAY DIFFRACTIONc_mcbond_it1.1421.5
X-RAY DIFFRACTIONc_scbond_it1.9972
X-RAY DIFFRACTIONc_mcangle_it1.6432
X-RAY DIFFRACTIONc_scangle_it2.7942.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2cam.partoph19x_p450_fe3+_CN.hem
X-RAY DIFFRACTION3param19x_p450_weak_3+_CN.hemecam.top
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION5CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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