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- PDB-3l61: Crystal structure of substrate-free P450cam at 200 mM [K+] -

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Basic information

Entry
Database: PDB / ID: 3l61
TitleCrystal structure of substrate-free P450cam at 200 mM [K+]
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / cytochrome P450 / P450cam / camphor / substrate-free / open conformation / Metal-binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLee, Y.-T. / Wilson, R.F. / Rupniewski, I. / Goodin, D.B.
CitationJournal: Biochemistry / Year: 2010
Title: P450cam visits an open conformation in the absence of substrate.
Authors: Lee, Y.T. / Wilson, R.F. / Rupniewski, I. / Goodin, D.B.
History
DepositionDec 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1732
Polymers46,5571
Non-polymers6161
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.606, 73.825, 92.428
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 Camphor 5-monooxygenase / Cytochrome P450-cam / P450cam


Mass: 46556.816 Da / Num. of mol.: 1 / Mutation: C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 12-22% PEG 8000, 0.05 M Tris, 200 mM KCl, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2009 / Details: Rh coated flat mirror
RadiationMonochromator: side scattering I-beam bent single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→46.2 Å / Num. all: 72274 / Num. obs: 72274 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 3.9 / Num. unique all: 10424 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of P450cam complexed with a tethered substrate analog, unpublished

Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.258 / SU ML: 0.048 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21609 3635 5 %RANDOM
Rwork0.19689 ---
obs0.19788 68435 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.989 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å2-0 Å2
2---0.13 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 43 407 3585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223431
X-RAY DIFFRACTIONr_angle_refined_deg1.2842.0074717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1935447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14824.012167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83615586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4051528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212682
X-RAY DIFFRACTIONr_mcbond_it0.6661.52067
X-RAY DIFFRACTIONr_mcangle_it1.24723385
X-RAY DIFFRACTIONr_scbond_it1.91531364
X-RAY DIFFRACTIONr_scangle_it3.1194.51304
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 229 -
Rwork0.305 4942 -
obs--99.94 %

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