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- PDB-2qbm: Crystal structure of the P450cam G248T mutant in the cyanide boun... -

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Basic information

Entry
Database: PDB / ID: 2qbm
TitleCrystal structure of the P450cam G248T 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: 1.8 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)48,4275
Polymers47,5931
Non-polymers8344
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.800, 64.600, 105.500
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 Cytochrome P450-cam / Camphor 5-monooxygenase / P450cam


Mass: 47592.996 Da / Num. of mol.: 1 / Mutation: G248T
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, 420 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.: 416 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
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: 0.9796 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2007 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 40676 / Num. obs: 40676 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.055 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.425 / % possible all: 95

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345softwaredata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1akd

1akd


Resolution: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.609 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22045 2034 5 %RANDOM
Rwork0.17627 ---
obs0.1785 38641 100 %-
all-40675 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 57 416 3688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223352
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.014573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38323.899159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49715550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9671526
X-RAY DIFFRACTIONr_chiral_restr0.1150.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022592
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.21770
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22298
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2347
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7711.52032
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45323294
X-RAY DIFFRACTIONr_scbond_it2.50331320
X-RAY DIFFRACTIONr_scangle_it3.9464.51279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 134 -
Rwork0.245 2544 -
obs--100 %

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