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- PDB-6ci2: Crystal structure of the formyltransferase PseJ from Anoxybacillu... -

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Basic information

Entry
Database: PDB / ID: 6ci2
TitleCrystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis
Componentsformyltransferase PseJ
KeywordsTRANSFERASE / formyltransferase
Biological speciesAnoxybacillus kamchatkensis G10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsReimer, J.M. / Jiang, J. / Harb, I. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-148472 Canada
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structural Insight into a Novel Formyltransferase and Evolution to a Nonribosomal Peptide Synthetase Tailoring Domain.
Authors: Reimer, J.M. / Harb, I. / Ovchinnikova, O.G. / Jiang, J. / Whitfield, C. / Schmeing, T.M.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 8, 2020Group: 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: formyltransferase PseJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9823
Polymers22,6911
Non-polymers2912
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.630, 77.510, 41.730
Angle α, β, γ (deg.)90.000, 103.840, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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Components

#1: Protein formyltransferase PseJ


Mass: 22690.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus kamchatkensis G10 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.36 Å3/Da / Density % sol: 63.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.6, 30.67% PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→59.5 Å / Num. obs: 21304 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.9330842615 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 8
Reflection shellResolution: 1.96→2 Å / Rmerge(I) obs: 0.124

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Processing

Software
NameVersionClassification
PHENIXdev_3042refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ES6

5es6


Resolution: 1.96→31.33 Å / SU ML: 0.2076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.395
RfactorNum. reflection% reflection
Rfree0.2229 2132 10.01 %
Rwork0.1799 --
obs0.1842 21296 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.03 Å2
Refinement stepCycle: LAST / Resolution: 1.96→31.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 17 132 1730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01711638
X-RAY DIFFRACTIONf_angle_d1.32952218
X-RAY DIFFRACTIONf_chiral_restr0.0916234
X-RAY DIFFRACTIONf_plane_restr0.009276
X-RAY DIFFRACTIONf_dihedral_angle_d20.4564975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-20.23631530.20121249X-RAY DIFFRACTION97.97
2-2.050.2491320.19611298X-RAY DIFFRACTION99.93
2.05-2.110.19661370.19211272X-RAY DIFFRACTION99.86
2.11-2.170.21291520.18071259X-RAY DIFFRACTION99.93
2.17-2.240.25681390.191288X-RAY DIFFRACTION100
2.24-2.320.22731400.18831294X-RAY DIFFRACTION99.93
2.32-2.410.25391510.17941256X-RAY DIFFRACTION99.93
2.41-2.520.23791360.18311308X-RAY DIFFRACTION99.93
2.52-2.650.2191440.18981262X-RAY DIFFRACTION100
2.65-2.820.27211440.2011296X-RAY DIFFRACTION99.93
2.82-3.040.25841450.21131275X-RAY DIFFRACTION100
3.04-3.340.24961350.18461286X-RAY DIFFRACTION100
3.34-3.820.21641450.18061318X-RAY DIFFRACTION100
3.82-4.820.17631440.14821276X-RAY DIFFRACTION99.23
4.82-31.340.20291350.16881227X-RAY DIFFRACTION92.65

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