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- PDB-1rf9: Crystal structure of cytochrome P450-cam with a fluorescent probe... -

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Basic information

Entry
Database: PDB / ID: 1rf9
TitleCrystal structure of cytochrome P450-cam with a fluorescent probe D-4-AD (Adamantane-1-carboxylic acid-5-dimethylamino-naphthalene-1-sulfonylamino-butyl-amide)
ComponentsCytochrome P450-cam
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / CONFORMATIONAL STATES / SUBSTRATE-LINKED SENSITIZERS / SUBSTRATE-BINDING / DANSYL / ADAMANTANE / ADAMANTANE-1-CARBOXYLIC ACID [4-(5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO)-BUTYL]-AMIDE / CHANNEL
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
Chem-DBR / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHays, A.-M.A. / Dunn, A.R. / Gray, H.B. / Stout, C.D. / Goodin, D.B.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Conformational States of Cytochrome P450cam Revealed by Trapping of synthetic Molecular Wires
Authors: Hays, A.-M.A. / Dunn, A.R. / Chiu, R. / Gray, H.B. / Stout, C.D. / Goodin, D.B.
History
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: Cytochrome P450-cam
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1244
Polymers46,9611
Non-polymers1,1623
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.126, 75.112, 93.165
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 / Camphor 5-monooxygenase / P450cam


Mass: 46961.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: CAMC, CYP101 / Plasmid: PUS200 / Production host: Escherichia coli (E. coli) / Strain (production host): TBY / 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-DBR / ADAMANTANE-1-CARBOXYLIC ACID-5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO-BUTYL-AMIDE


Mass: 483.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O3S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CITRATE, PEG, KCL, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 38960 / Num. obs: 32283 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 3.15 % / Biso Wilson estimate: 19.83 Å2 / Rsym value: 0.063 / Net I/σ(I): 17.9
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.34 / % possible all: 88.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPP

2cpp


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.227 1632 RANDOM
Rwork0.196 --
obs0.198 32283 -
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 81 327 3607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.275
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.89

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