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

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Basic information

Entry
Database: PDB / ID: 6edk
TitleCrystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis with N10-formyltetrahydrofolate
ComponentsFormyltransferase PseJ
KeywordsTRANSFERASE / formyltransferase
Function / homologyChem-1YA
Function and homology information
Biological speciesAnoxybacillus kamchatkensis G10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsReimer, J.M. / 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
DepositionAug 9, 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 11, 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)26,3744
Polymers25,6091
Non-polymers7653
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.200, 77.300, 40.460
Angle α, β, γ (deg.)90.000, 103.900, 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

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Components

#1: Protein Formyltransferase PseJ


Mass: 25609.049 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: Chemical ChemComp-1YA / N-{4-[{[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}(formyl)amino]benzoyl}-L-glutamic acid


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 0.1M MES pH 6.5, 26% PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→47.18 Å / Num. obs: 26389 / % possible obs: 97.9 % / Redundancy: 6 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.763 / Num. unique obs: 1627

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CI2
Resolution: 1.8→47.18 Å / SU ML: 0.1959 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9222
RfactorNum. reflection% reflection
Rfree0.1938 2639 10 %
Rwork0.1681 --
obs0.1706 26385 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 51 106 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01691707
X-RAY DIFFRACTIONf_angle_d1.35272313
X-RAY DIFFRACTIONf_chiral_restr0.0855240
X-RAY DIFFRACTIONf_plane_restr0.0085289
X-RAY DIFFRACTIONf_dihedral_angle_d13.58431008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.2971550.27681303X-RAY DIFFRACTION98.91
1.83-1.870.2951230.26441246X-RAY DIFFRACTION98.49
1.87-1.910.31231520.24681216X-RAY DIFFRACTION97.44
1.91-1.950.25031310.23251221X-RAY DIFFRACTION95.62
1.95-1.990.22821470.21461250X-RAY DIFFRACTION98.66
1.99-2.040.22741240.20871270X-RAY DIFFRACTION98.59
2.04-2.10.23351570.19821224X-RAY DIFFRACTION98.57
2.1-2.160.21371340.19681267X-RAY DIFFRACTION98.45
2.16-2.230.23181450.17241258X-RAY DIFFRACTION98.66
2.23-2.310.18931190.17491229X-RAY DIFFRACTION96.35
2.31-2.40.20551460.16671227X-RAY DIFFRACTION96.15
2.4-2.510.2121450.16651253X-RAY DIFFRACTION98.8
2.51-2.640.2161400.16971251X-RAY DIFFRACTION98.72
2.64-2.810.1871400.16991258X-RAY DIFFRACTION98.17
2.81-3.030.20211260.16971221X-RAY DIFFRACTION95.87
3.03-3.330.15821390.161277X-RAY DIFFRACTION98.13
3.33-3.810.16181390.15771261X-RAY DIFFRACTION98.31
3.81-4.80.15771340.13521240X-RAY DIFFRACTION95.55
4.8-47.190.20711430.16641274X-RAY DIFFRACTION97.32
Refinement TLS params.Method: refined / Origin x: 35.3506301031 Å / Origin y: 18.4195241171 Å / Origin z: 6.93756437028 Å
111213212223313233
T0.15558424983 Å2-0.0266658533565 Å20.0153041522686 Å2-0.183126141632 Å2-0.0162230704393 Å2--0.166826967925 Å2
L0.529637959809 °20.182605467755 °20.47226570633 °2-0.443757762074 °20.128054755986 °2--1.05388181991 °2
S0.0231156997847 Å °-0.0177202103295 Å °-0.037873048712 Å °0.0323694960817 Å °-0.00551176934577 Å °-0.0130942609059 Å °0.0793037506715 Å °-0.1638094723 Å °5.47096386284E-10 Å °
Refinement TLS groupSelection details: all

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