[English] 日本語
Yorodumi
- PDB-5ufy: Structure of Streptococcus pneumoniae peptidoglycan O-acetyltrans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ufy
TitleStructure of Streptococcus pneumoniae peptidoglycan O-acetyltransferase A (OatA) C-terminal catalytic domain
ComponentsAcyltransferase
KeywordsTRANSFERASE / atytpical alpha/beta hydrolase / catalytic triad
Function / homology
Function and homology information


: / lipopolysaccharide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / membrane => GO:0016020 / membrane
Similarity search - Function
Acyltransferase 3 domain / Acyltransferase family / SGNH hydrolase superfamily
Similarity search - Domain/homology
Acyltransferase / Acyltransferase 3 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsSychantha, D. / Jones, C. / Little, D.J. / Moynihan, P.J. / Robinson, H. / Galley, N.F. / Roper, D.I. / Dowson, C.G. / Howell, P.L. / Clarke, A.J.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Glycomics Network Canada
Canadian Institute for Health ResearchTGC 114045 Canada
Canadian Institute for Health ResearchMOP 43998 Canada
CitationJournal: PLoS Pathog. / Year: 2017
Title: In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA).
Authors: Sychantha, D. / Jones, C.S. / Little, D.J. / Moynihan, P.J. / Robinson, H. / Galley, N.F. / Roper, D.I. / Dowson, C.G. / Howell, P.L. / Clarke, A.J.
History
DepositionJan 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4402
Polymers24,4171
Non-polymers231
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.203, 70.203, 135.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-957-

HOH

21A-979-

HOH

-
Components

#1: Protein Acyltransferase


Mass: 24417.191 Da / Num. of mol.: 1 / Mutation: UNP residues 421-605
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: oatA_2, oatA, oatA_1, oatA_3, ERS020138_01729, ERS020158_01919, ERS020525_00845, ERS020528_00979, ERS020532_00615, ERS020726_01157, ERS020726_01160, ERS020726_01165, ERS021733_04500, ERS232524_00457
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: A0A0T7JIN8, UniProt: Q8CY83*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 1.71 Å3/Da / Density % sol: 28.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1.8 M NaH2PO4/K2HPO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 65286 / % possible obs: 99.1 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 64.2
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 13.2 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→40.051 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.46
RfactorNum. reflection% reflection
Rfree0.1681 1991 3.09 %
Rwork0.1502 --
obs0.1508 64409 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.12→40.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 1 243 1610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061411
X-RAY DIFFRACTIONf_angle_d0.9391916
X-RAY DIFFRACTIONf_dihedral_angle_d14.489517
X-RAY DIFFRACTIONf_chiral_restr0.075225
X-RAY DIFFRACTIONf_plane_restr0.007247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1197-1.14770.20181370.20814281X-RAY DIFFRACTION96
1.1477-1.17870.19741390.17534306X-RAY DIFFRACTION97
1.1787-1.21340.18651390.17034370X-RAY DIFFRACTION97
1.2134-1.25250.191370.1664352X-RAY DIFFRACTION98
1.2525-1.29730.16531390.16954374X-RAY DIFFRACTION98
1.2973-1.34930.17681400.16414404X-RAY DIFFRACTION98
1.3493-1.41070.18991420.16054419X-RAY DIFFRACTION99
1.4107-1.4850.15911410.15474446X-RAY DIFFRACTION99
1.485-1.57810.181440.14464464X-RAY DIFFRACTION99
1.5781-1.69990.14771430.14634505X-RAY DIFFRACTION100
1.6999-1.8710.16231440.15244522X-RAY DIFFRACTION100
1.871-2.14170.15251450.13964557X-RAY DIFFRACTION100
2.1417-2.69830.1681470.14224607X-RAY DIFFRACTION100
2.6983-40.07630.16891540.14644811X-RAY DIFFRACTION100
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)
11.5798-0.87020.4641.41110.10151.7383-0.01440.07140.0489-0.0175-0.0045-0.1272-0.01680.13550.00830.0613-0.01320.01920.0897-0.00430.0875-10.277527.6017-23.7559
23.85581.01850.42043.2950.2424.9729-0.01320.11890.0355-0.19160.0878-0.0345-0.0247-0.218-0.08370.03660.01970.02190.0405-0.020.0555-16.675227.9441-28.8976
32.5011-0.21732.22983.02851.6616.351-0.1681-0.18050.13540.10450.0468-0.0803-0.1871-0.12840.14010.0754-0.00270.00320.0687-0.00230.0814-18.983732.9951-11.8007
41.99930.50822.43664.2980.65758.35020.0060.00960.0106-0.0344-0.00410.0714-0.058-0.0982-0.02170.0358-0.00970.01950.094-0.00690.0706-22.947725.7656-24.3925
53.17-1.2931.46042.40662.27516.6708-0.0331-0.24370.05870.17480.2619-0.2497-0.00470.1853-0.21750.0805-0.0161-0.01190.08890.00040.0969-9.031425.7557-2.0689
61.93860.12311.18250.57410.04761.92420.0962-0.0887-0.12450.0862-0.004-0.07360.1311-0.0029-0.07620.0902-0.0094-0.02330.08070.00850.0889-12.858420.6775-8.4661
74.6459-1.37663.93531.6702-0.84043.54060.24040.3236-0.32760.0389-0.0173-0.03460.27930.2169-0.26170.11040.01080.0070.1056-0.01420.1-13.398616.0441-20.2103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 427 through 476 )
2X-RAY DIFFRACTION2chain 'A' and (resid 477 through 487 )
3X-RAY DIFFRACTION3chain 'A' and (resid 488 through 506 )
4X-RAY DIFFRACTION4chain 'A' and (resid 507 through 515 )
5X-RAY DIFFRACTION5chain 'A' and (resid 516 through 527 )
6X-RAY DIFFRACTION6chain 'A' and (resid 528 through 575 )
7X-RAY DIFFRACTION7chain 'A' and (resid 576 through 605 )

+
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