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- PDB-5vws: Ligand free structure of Cytochrome P450 TbtJ1 -

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Basic information

Entry
Database: PDB / ID: 5vws
TitleLigand free structure of Cytochrome P450 TbtJ1
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Thiomuracin GZ
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
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 / Cytochrome P450
Similarity search - Component
Biological speciesThermobispora bispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.411 Å
AuthorsGober, J.G. / Ghodge, S.V. / Brustad, E.M. / Bowers, A.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1552718 United States
Beckman Institute United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA016086 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: P450-Mediated Non-natural Cyclopropanation of Dehydroalanine-Containing Thiopeptides.
Authors: Gober, J.G. / Ghodge, S.V. / Bogart, J.W. / Wever, W.J. / Watkins, R.R. / Brustad, E.M. / Bowers, A.A.
History
DepositionMay 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2742
Polymers44,6581
Non-polymers6161
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.316, 95.316, 126.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cytochrome P450 /


Mass: 44657.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51) (bacteria)
Strain: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51
Gene: Tbis_0546 / Production host: Escherichia coli (E. coli) / References: UniProt: D6Y4Z8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1 M (NH4)2SO4 1 % PEG 3350 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→27.221 Å / Num. obs: 21196 / % possible obs: 91.43 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
KYLINdata reduction
KYLINdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WIO

2wio


Resolution: 2.411→27.221 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 24.44
RfactorNum. reflection% reflection
Rfree0.2808 1064 5.02 %
Rwork0.2084 --
obs0.212 21196 91.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.37 Å2 / Biso mean: 22.9674 Å2 / Biso min: 4.08 Å2
Refinement stepCycle: final / Resolution: 2.411→27.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 73 96 3172
Biso mean--14.38 20.25 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093128
X-RAY DIFFRACTIONf_angle_d1.024260
X-RAY DIFFRACTIONf_chiral_restr0.046458
X-RAY DIFFRACTIONf_plane_restr0.008557
X-RAY DIFFRACTIONf_dihedral_angle_d14.7451851
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4107-2.52030.3751940.34122163225780
2.5203-2.65310.37951470.29622550269795
2.6531-2.81910.32671410.25962541268294
2.8191-3.03660.31121460.24152535268194
3.0366-3.34160.33011280.21182569269794
3.3416-3.8240.26521250.17782609273494
3.824-4.81360.20541370.14692589272693
4.8136-27.22280.22761460.16482576272288

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