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- PDB-6ci5: Crystal structure of the formyltransferase PseJ from Anoxybacillu... -

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Basic information

Entry
Database: PDB / ID: 6ci5
TitleCrystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis in complex with UDP-4,6-dideoxy-4-formamido-L-AltNAc and tetrahydrofolate
Componentsformyltransferase PseJ
KeywordsTRANSFERASE / formyltransferase
Function / homologyChem-1YJ / Chem-F5G
Function and homology information
Biological speciesAnoxybacillus kamchatkensis G10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00003052726 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
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

Downloads & links

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Assembly

Deposited unit
A: formyltransferase PseJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7694
Polymers25,6091
Non-polymers1,1603
Water55831
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)96.420, 73.780, 41.800
Angle α, β, γ (deg.)90.000, 103.470, 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-F5G / (2R,3R,4S,5R,6S)-3-(acetylamino)-5-(formylamino)-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 618.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28N4O16P2
#4: Chemical ChemComp-1YJ / N-[4-({[(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 25.6% 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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→47.23 Å / Num. obs: 32206 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 48.8393855317 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.984 / Num. unique obs: 1720

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Processing

Software
NameVersionClassification
phenix.refinedev_2689refinement
PHENIXdev_2689refinement
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CI2

6ci2


Resolution: 2.00003052726→46.8838402268 Å / SU ML: 0.312089467255 / Cross valid method: FREE R-VALUE / σ(F): 1.47364596753 / Phase error: 30.9228387233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239543829849 1925 9.9771949829 %
Rwork0.217847174875 17369 -
obs0.220023852975 19294 99.9274911954 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.0064049426 Å2
Refinement stepCycle: LAST / Resolution: 2.00003052726→46.8838402268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 58 31 1670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002051620442791682
X-RAY DIFFRACTIONf_angle_d0.5395533322242285
X-RAY DIFFRACTIONf_chiral_restr0.0426805212405244
X-RAY DIFFRACTIONf_plane_restr0.00238724576518280
X-RAY DIFFRACTIONf_dihedral_angle_d16.6324302796973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.4129863947551320.367191670131226X-RAY DIFFRACTION100
2.05-2.10550.3698454275131340.3417795225971246X-RAY DIFFRACTION99.8552821997
2.1055-2.16740.3239177667391380.3217680325231231X-RAY DIFFRACTION99.8541210795
2.1674-2.23740.3017950857851390.3166352657621240X-RAY DIFFRACTION99.9275362319
2.2374-2.31740.3365370051241470.2882130034721218X-RAY DIFFRACTION99.7807017544
2.3174-2.41010.2819503846691250.2795982304441227X-RAY DIFFRACTION99.8522895126
2.4101-2.51980.3000451246421420.2644733007231231X-RAY DIFFRACTION100
2.5198-2.65270.2701602389241380.2683315481121255X-RAY DIFFRACTION99.9282639885
2.6527-2.81880.3326525132381390.2672372889471233X-RAY DIFFRACTION100
2.8188-3.03640.3103908754991360.2713601086781256X-RAY DIFFRACTION100
3.0364-3.34190.2564344523971350.2366962215231232X-RAY DIFFRACTION100
3.3419-3.82530.206743724581390.2049037369241249X-RAY DIFFRACTION100
3.8253-4.81870.1879876304421380.1684724751261248X-RAY DIFFRACTION100
4.8187-46.89670.2048567857181430.1790192536721277X-RAY DIFFRACTION99.9296270232
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.931110195781.500707726361.131497322263.422656770821.585774817774.136537097030.336215461471-0.00874891108491-0.2875265441960.282011485248-0.3386403422370.3502432631931.32585576137-1.13090543570.02789893290.687239537699-0.266108724642-0.021618841210.603663771107-0.01909447682390.45529369742230.688887702411.17022405254.10042172602
22.500608147940.7421042837172.099044628038.60671215272.129239308617.911243420320.1454436017340.0547131828139-0.2417269617570.378842749649-0.0455236097888-0.142401992920.414436660714-0.0978437913489-0.112845419130.233664009166-0.004449031489910.01124197252170.356500179316-0.02000619136950.36025235293641.18042796422.2357705968.7460414175
33.56455136790.2129707812670.2997261400315.71557934761-0.2930854790237.865964087720.170214526140.01998331829780.3900552791690.244251855937-0.1849014680550.653699028798-0.859477297217-1.16340484707-0.03159009004060.422240567110.103521883008-0.0236027261310.594730374033-0.08343583244860.47298777287834.026151024831.678648722511.4948995518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 214 )

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