[English] 日本語
Yorodumi
- PDB-7n7c: crystal structure of the N-formyltransferase HCAN_0200 from helic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n7c
Titlecrystal structure of the N-formyltransferase HCAN_0200 from helicobacter canadensis in complex with folinic acid and dTDP-3-aminoquinovose
ComponentsFormyl_trans_N domain-containing protein
KeywordsTRANSFERASE / folinic acid / formyltransferase / aminoquinovose
Function / homologymethionyl-tRNA formyltransferase activity / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / cytosol / Chem-FON / : / Chem-T3Q / Formyl transferase N-terminal domain-containing protein
Function and homology information
Biological speciesHelicobacter canadensis MIT 98-5491 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHeisdorf, C.J. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis.
Authors: Heisdorf, C.J. / Griffiths, W.A. / Thoden, J.B. / Holden, H.M.
History
DepositionJun 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formyl_trans_N domain-containing protein
B: Formyl_trans_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,43711
Polymers66,1312
Non-polymers2,3069
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-5 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.997, 74.039, 82.328
Angle α, β, γ (deg.)90.000, 115.040, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Formyl_trans_N domain-containing protein


Mass: 33065.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter canadensis MIT 98-5491 (bacteria)
Gene: HCAN_0200 / Production host: Escherichia coli (E. coli) / References: UniProt: C5ZW02

-
Non-polymers , 5 types, 450 molecules

#2: Chemical ChemComp-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N7O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-T3Q / [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate / thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose


Mass: 547.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H27N3O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 11-14% PEG-8000, 2% DMSO, 100 mM homopipes (pH 5) Crystals soaked in 26% PEG-8000, 600 mM NaCl, 5 mM folinic acid, 10 mM dTDP-3-aminoquinovose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 46424 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rsym value: 0.073 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 6240 / Rsym value: 0.347 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7n7a

7n7a


Resolution: 2→29.2 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.885 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 2336 5 %RANDOM
Rwork0.1818 ---
obs0.1843 44088 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.08 Å2 / Biso mean: 26.632 Å2 / Biso min: 11.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4480 0 152 441 5073
Biso mean--33.37 31.09 -
Num. residues----540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134745
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174286
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.6426411
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5749990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2735540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04624.524252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28215835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4151510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02999
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 170 -
Rwork0.3 3235 -
all-3405 -
obs--97.99 %

+
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://pdbjlvh1.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