[English] 日本語
Yorodumi
- PDB-6ci4: Crystal structure of the formyltransferase PseJ from Anoxybacillu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ci4
TitleCrystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis soaked with UDP-4-amino-4,6-dideoxy-L-AltNAc
Componentsformyltransferase PseJ
KeywordsTRANSFERASE / formyltransferase
Function / homologyChem-F5P
Function and homology information
Biological speciesAnoxybacillus kamchatkensis G10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82406793237 Å
AuthorsHarb, I. / Reimer, J.M. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: formyltransferase PseJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1992
Polymers25,6091
Non-polymers5901
Water1,65792
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)96.425, 73.780, 41.805
Angle α, β, γ (deg.)90.000, 103.474, 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

#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-F5P / (2R,3R,4S,5R,6S)-3-(acetylamino)-5-amino-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 / UDP-4-amino-4,6-dideoxy-L-AltNAc


Mass: 590.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28N4O15P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 28.4% PEG5000 MME

-
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: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→46.89 Å / Num. obs: 23891 / % possible obs: 93.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 33.9361522933 Å2 / Net I/σ(I): 12.1
Reflection shellResolution: 1.82→1.85 Å / Num. unique obs: 1025 / CC1/2: 0.691 / Rpim(I) all: 0.398

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CI2

6ci2


Resolution: 1.82406793237→46.8854873102 Å / SU ML: 0.243767715036 / Cross valid method: FREE R-VALUE / σ(F): 1.37584249725 / Phase error: 24.4032592997
RfactorNum. reflection% reflection
Rfree0.211125495844 2379 9.96606761342 %
Rwork0.185728548408 --
obs0.188269814514 23891 93.8768286928 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.5865318402 Å2
Refinement stepCycle: LAST / Resolution: 1.82406793237→46.8854873102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 38 92 1719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01148059932861670
X-RAY DIFFRACTIONf_angle_d1.21671096942268
X-RAY DIFFRACTIONf_chiral_restr0.060086822911244
X-RAY DIFFRACTIONf_plane_restr0.0067884249705280
X-RAY DIFFRACTIONf_dihedral_angle_d19.1789959165974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8241-1.86130.3759914774511130.346155690341018X-RAY DIFFRACTION75.6016042781
1.8613-1.90180.3012302403451320.3233896386361188X-RAY DIFFRACTION88.5906040268
1.9018-1.9460.3061697397451370.2937082200311230X-RAY DIFFRACTION93.3743169399
1.946-1.99470.2484988430491410.2614709898261282X-RAY DIFFRACTION93.9273927393
1.9947-2.04860.2587507561321420.232724227391273X-RAY DIFFRACTION95.4790823212
2.0486-2.10890.2436168948841430.209605771491332X-RAY DIFFRACTION98.9268947015
2.1089-2.1770.1917043485991500.1917383911021310X-RAY DIFFRACTION98.9159891599
2.177-2.25480.2094678827861490.1822453219171309X-RAY DIFFRACTION98.3805668016
2.2548-2.3450.2263278870721430.1772618827911341X-RAY DIFFRACTION97.7602108037
2.345-2.45180.2286445294481390.1764584343071246X-RAY DIFFRACTION94.6684894053
2.4518-2.5810.2122051890981480.1832006727471330X-RAY DIFFRACTION98.0756469808
2.581-2.74270.2114903241861480.1850397354551319X-RAY DIFFRACTION97.995991984
2.7427-2.95440.2546516483161360.2030937334991305X-RAY DIFFRACTION96.5170797053
2.9544-3.25170.2200771673181390.1884019087011218X-RAY DIFFRACTION91.0127431254
3.2517-3.72210.2235987351681410.1879835815371265X-RAY DIFFRACTION92.8665785997
3.7221-4.68870.1493348397641310.1536221577331206X-RAY DIFFRACTION88.2508250825
4.6887-46.9010.1971643582671470.1679804849821320X-RAY DIFFRACTION95.9450621321
Refinement TLS params.Method: refined / Origin x: 35.0366418687 Å / Origin y: 20.2339551917 Å / Origin z: 7.16782828339 Å
111213212223313233
T0.276758589972 Å2-0.02436619392 Å20.00951708769985 Å2-0.308184386673 Å20.0011125959634 Å2--0.282266191064 Å2
L0.828381921889 °20.0711051878483 °20.106765405235 °2-1.2212714022 °20.361320215179 °2--1.58083443106 °2
S0.05850576294 Å °-0.000459662651301 Å °0.0203711361418 Å °0.0960590309077 Å °-0.0949538631719 Å °0.0406639091453 Å °0.124164648754 Å °-0.198952077381 Å °-1.10709986203E-5 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more