[English] 日本語
Yorodumi
- PDB-6wye: Crystal structure of Neisseria gonorrhoeae serine acetyltransfera... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wye
TitleCrystal structure of Neisseria gonorrhoeae serine acetyltransferase (CysE)
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / CysE / Serine acetyltransferase / Neisseria / Gonorrhoea
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / Serine acetyltransferase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHicks, J.L. / Oldham, K.E. / Summers, E.L. / Prentice, E.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)19/602 New Zealand
CitationJournal: Biochem.J. / Year: 2022
Title: Serine acetyltransferase from Neisseria gonorrhoeae; structural and biochemical basis of inhibition.
Authors: Oldham, K.E.A. / Prentice, E.J. / Summers, E.L. / Hicks, J.L.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 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 1.2Jan 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
D: Serine acetyltransferase
E: Serine acetyltransferase
F: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,89718
Polymers189,9556
Non-polymers94212
Water9,692538
1
A: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules

A: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules

E: Serine acetyltransferase
hetero molecules

E: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,89718
Polymers189,9556
Non-polymers94212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area20770 Å2
ΔGint-184 kcal/mol
Surface area49800 Å2
MethodPISA
2
B: Serine acetyltransferase
D: Serine acetyltransferase
F: Serine acetyltransferase
hetero molecules

B: Serine acetyltransferase
D: Serine acetyltransferase
F: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,89718
Polymers189,9556
Non-polymers94212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area20500 Å2
ΔGint-173 kcal/mol
Surface area49390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.897, 93.867, 102.019
Angle α, β, γ (deg.)90.00, 91.29, 90.00
Int Tables number3
Space group name H-MP121
Symmetry operation#1: x,y,z
#2: -x,y,-z

-
Components

#1: Protein
Serine acetyltransferase


Mass: 31659.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria)
Gene: cysE, E8M63_06755, F0T10_08440, F0T11_08395, F0T12_08425, NCTC13805_01597, WHOF_01434, WHOF_01635
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3FX11, serine O-acetyltransferase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 28% (v/v) Tacsimate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.01→46.93 Å / Num. obs: 97704 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 34.69 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 17.2
Reflection shellResolution: 2.01→2.04 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4841 / CC1/2: 0.917 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.16_3549)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GVD

3gvd


Resolution: 2.01→43.11 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 4749 4.88 %
Rwork0.183 --
obs0.1849 97327 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11130 0 60 538 11728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811436
X-RAY DIFFRACTIONf_angle_d0.8515531
X-RAY DIFFRACTIONf_dihedral_angle_d12.513918
X-RAY DIFFRACTIONf_chiral_restr0.0571786
X-RAY DIFFRACTIONf_plane_restr0.0062025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.03290.27011400.22083097X-RAY DIFFRACTION100
2.0329-2.05680.28121470.21373093X-RAY DIFFRACTION100
2.0568-2.08190.2721370.2193101X-RAY DIFFRACTION100
2.0819-2.10820.28811480.21773111X-RAY DIFFRACTION100
2.1082-2.1360.26541310.21863122X-RAY DIFFRACTION100
2.136-2.16520.26981660.21413100X-RAY DIFFRACTION100
2.1652-2.19610.28391740.20942999X-RAY DIFFRACTION100
2.1961-2.22890.29421690.20473104X-RAY DIFFRACTION100
2.2289-2.26380.38991210.29252838X-RAY DIFFRACTION92
2.2638-2.30090.24411470.19663115X-RAY DIFFRACTION100
2.3009-2.34050.23681600.1843072X-RAY DIFFRACTION100
2.3405-2.38310.21711350.18293099X-RAY DIFFRACTION100
2.3831-2.42890.22681690.18383109X-RAY DIFFRACTION100
2.4289-2.47850.21431940.19073016X-RAY DIFFRACTION100
2.4785-2.53240.20781570.18293099X-RAY DIFFRACTION100
2.5324-2.59130.27251690.18993090X-RAY DIFFRACTION100
2.5913-2.65610.24581610.19493074X-RAY DIFFRACTION100
2.6561-2.72790.21121660.19513071X-RAY DIFFRACTION100
2.7279-2.80810.25481630.19523102X-RAY DIFFRACTION100
2.8081-2.89880.21311680.19973098X-RAY DIFFRACTION100
2.8988-3.00230.26381530.20493097X-RAY DIFFRACTION100
3.0023-3.12250.23841540.2013113X-RAY DIFFRACTION100
3.1225-3.26460.26291700.19433073X-RAY DIFFRACTION100
3.2646-3.43660.19821300.1993120X-RAY DIFFRACTION100
3.4366-3.65180.22511390.18543150X-RAY DIFFRACTION100
3.6518-3.93360.19262020.1583070X-RAY DIFFRACTION100
3.9336-4.32920.17652010.15063068X-RAY DIFFRACTION100
4.3292-4.95480.1671640.13733094X-RAY DIFFRACTION99
4.9548-6.23950.22861640.17673124X-RAY DIFFRACTION100
6.2395-43.110.21851500.17423159X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 37.491 Å / Origin y: 54.6632 Å / Origin z: 26.2118 Å
111213212223313233
T0.2613 Å20.0039 Å2-0.0243 Å2-0.2859 Å20.0074 Å2--0.2833 Å2
L-0.0799 °2-0.0083 °2-0.0282 °2-0.2827 °20.0161 °2--0.0674 °2
S-0.0022 Å °-0.0207 Å °-0.0097 Å °-0.0091 Å °0.0071 Å °-0.0107 Å °0.0177 Å °0.0257 Å °-0.0048 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