[English] 日本語
Yorodumi
- PDB-7s3w: Crystal structure of an N-acetyltransferase from Helicobacter pul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s3w
TitleCrystal structure of an N-acetyltransferase from Helicobacter pullorum in the presence of Coenzyme A and dTDP-3-amino-3,6-dideoxy-D-galactose
ComponentsN-acetyltransferase
KeywordsTRANSFERASE
Function / homologyOXIDIZED COENZYME A / Chem-T3F
Function and homology information
Biological speciesHelicobacter pullorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsGriffiths, W.A. / Spencer, K.D. / 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: Biochemical investigation of an N-acetyltransferase from Helicobacter pullorum.
Authors: Griffiths, W.A. / Spencer, K.D. / Thoden, J.B. / Holden, H.M.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
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: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7578
Polymers18,1551
Non-polymers1,6027
Water4,089227
1
A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,27124
Polymers54,4643
Non-polymers4,80621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area13110 Å2
ΔGint-27 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.441, 103.441, 103.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-207-

NA

21A-498-

HOH

31A-505-

HOH

41A-523-

HOH

51A-527-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein N-acetyltransferase


Mass: 18154.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pullorum (bacteria) / Strain: NAP8W25 / Gene: BA919_rs02330 / Production host: Escherichia coli (E. coli)

-
Non-polymers , 5 types, 234 molecules

#2: Chemical ChemComp-T3F / (3R,4S,5R,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-aminogalactose


Mass: 547.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N3O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CAO / OXIDIZED COENZYME A


Mass: 783.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11-18% PEG-3350, 200 mM KCl, 5 mM coenzyme A, 5 mM dTDP-3-amino-3,6-dideoxy-D-galactose, 100 mM HEPPS

-
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: Sep 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 50690 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rsym value: 0.043 / Net I/σ(I): 16.6
Reflection shellResolution: 1.25→1.35 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 10328 / Rsym value: 0.254 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7s3u

7s3u


Resolution: 1.25→29.88 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.567 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1663 2427 4.8 %RANDOM
Rwork0.1442 ---
obs0.1452 48263 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.21 Å2 / Biso mean: 10.689 Å2 / Biso min: 3.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.25→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 102 229 1438
Biso mean--13.37 25.29 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131314
X-RAY DIFFRACTIONr_bond_other_d00.0171228
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.71805
X-RAY DIFFRACTIONr_angle_other_deg1.3711.612880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5355168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.97525.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21515221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.511152
X-RAY DIFFRACTIONr_chiral_restr0.0810.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02237
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 171 -
Rwork0.261 3541 -
all-3712 -
obs--99.38 %

+
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