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- PDB-1geb: X-RAY CRYSTAL STRUCTURE AND CATALYTIC PROPERTIES OF THR252ILE MUT... -

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Basic information

Entry
Database: PDB / ID: 1geb
TitleX-RAY CRYSTAL STRUCTURE AND CATALYTIC PROPERTIES OF THR252ILE MUTANT OF CYTOCHROME P450CAM
ComponentsCYTOCHROME P450-CAM
KeywordsELECTRON TRANSPORT / Cytochrome P450cam / Monooxygenase
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 / Resolution: 2.03 Å
AuthorsHishiki, T. / Shimada, H. / Nagano, S. / Park, S.-Y. / Ishimura, Y.
CitationJournal: J.Biochem. / Year: 2000
Title: X-ray crystal structure and catalytic properties of Thr252Ile mutant of cytochrome P450cam: roles of Thr252 and water in the active center.
Authors: Hishiki, T. / Shimada, H. / Nagano, S. / Egawa, T. / Kanamori, Y. / Makino, R. / Park, S.Y. / Adachi, S. / Shiro, Y. / Ishimura, Y.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Nov 10, 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 1.5Oct 25, 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)47,5013
Polymers46,7321
Non-polymers7692
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.430, 103.440, 35.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450-CAM


Mass: 46732.129 Da / Num. of mol.: 1 / Mutation: T252I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / 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.: 1 / Source method: obtained synthetically / Formula: C10H16O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 6.5
Details: (NH4)2SO4, DTT, pH 6.5, SMALL TUBES, temperature 298K
Crystal grow
*PLUS
Temperature: 12-15 ℃ / pH: 7.5 / Method: unknown / Details: Poulos, T.L., (1982) J. Biol. Chem., 257, 10427.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM11KPi
2250 mM11KCl
350 mMdithiothreitol11
466-70 %satammonium sulphate12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 11, 2000 / Details: Monochro. SI-111
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. all: 108401 / Num. obs: 26966 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 8.5
Reflection shellResolution: 2.03→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3845 / Rsym value: 0.211 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 108401 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR3.851refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPP

2cpp


Resolution: 2.03→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 --RANDOM
Rwork0.187 ---
obs-26764 98.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 54 95 3358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_improper_angle_d0.85
LS refinement shellResolution: 2.03→2.13 Å
RfactorNum. reflection% reflection
Rfree0.277 214 -
Rwork0.249 --
obs-3965 84.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor Rfree: 0.277 / Rfactor Rwork: 0.249

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