[English] 日本語
Yorodumi
- PDB-4k3u: Peptidoglycan O-acetylesterase in action, 30 min -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k3u
TitlePeptidoglycan O-acetylesterase in action, 30 min
ComponentsGDSL-like Lipase/Acylhydrolase family protein
KeywordsHYDROLASE / alpha/Beta fold / peptidoglycan hydrolase
Function / homologyJelly Rolls - #1360 / SGNH hydrolase / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / :
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.158 Å
AuthorsWilliams, A.H. / Gomperts Boneca, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members.
Authors: Williams, A.H. / Veyrier, F.J. / Bonis, M. / Michaud, Y. / Raynal, B. / Taha, M.K. / White, S.W. / Haouz, A. / Boneca, I.G.
History
DepositionApr 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GDSL-like Lipase/Acylhydrolase family protein
B: GDSL-like Lipase/Acylhydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2965
Polymers81,5822
Non-polymers7153
Water7,728429
1
A: GDSL-like Lipase/Acylhydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0292
Polymers40,7911
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GDSL-like Lipase/Acylhydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2673
Polymers40,7911
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.120, 80.015, 122.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GDSL-like Lipase/Acylhydrolase family protein


Mass: 40790.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: Neisseria Meningitidis, NM4119_1198 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: L5SU74
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes pH 7.5 10-40% Peg 10,000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.158→48.54 Å / Num. obs: 3637 / % possible obs: 99.82 % / Observed criterion σ(F): 2.61 / Observed criterion σ(I): 2.61 / Biso Wilson estimate: 29.56 Å2 / Net I/σ(I): 9.91
Reflection shellResolution: 2.158→2.235 Å / Mean I/σ(I) obs: 9.91 / % possible all: 98.24

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXmodel building
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.158→48.539 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 3748 9.97 %
Rwork0.1595 --
obs0.166 -99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.158→48.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5295 0 45 429 5769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075483
X-RAY DIFFRACTIONf_angle_d1.0577442
X-RAY DIFFRACTIONf_dihedral_angle_d14.7031975
X-RAY DIFFRACTIONf_chiral_restr0.041807
X-RAY DIFFRACTIONf_plane_restr0.004968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1581-2.18540.34041320.22441194X-RAY DIFFRACTION95
2.1854-2.21420.3171430.21011229X-RAY DIFFRACTION100
2.2142-2.24450.27721350.18171223X-RAY DIFFRACTION100
2.2445-2.27660.22331310.17931243X-RAY DIFFRACTION100
2.2766-2.31050.26841500.16781226X-RAY DIFFRACTION100
2.3105-2.34660.22511500.18351240X-RAY DIFFRACTION100
2.3466-2.38510.30091590.17141183X-RAY DIFFRACTION100
2.3851-2.42620.28581380.17911277X-RAY DIFFRACTION100
2.4262-2.47040.26541370.17521225X-RAY DIFFRACTION100
2.4704-2.51790.25091170.18131259X-RAY DIFFRACTION100
2.5179-2.56930.24371290.15881258X-RAY DIFFRACTION100
2.5693-2.62510.25461360.15961227X-RAY DIFFRACTION100
2.6251-2.68620.24291320.1711255X-RAY DIFFRACTION100
2.6862-2.75330.22781380.16951253X-RAY DIFFRACTION100
2.7533-2.82780.25931370.16661240X-RAY DIFFRACTION100
2.8278-2.9110.26431340.17721259X-RAY DIFFRACTION100
2.911-3.00490.22491400.18221244X-RAY DIFFRACTION100
3.0049-3.11230.23511280.17521268X-RAY DIFFRACTION100
3.1123-3.23690.25391350.17821259X-RAY DIFFRACTION100
3.2369-3.38420.22541370.16771257X-RAY DIFFRACTION100
3.3842-3.56260.21371490.16541264X-RAY DIFFRACTION100
3.5626-3.78570.19261420.14771252X-RAY DIFFRACTION100
3.7857-4.07780.19471530.13771263X-RAY DIFFRACTION100
4.0778-4.48790.17211430.12981279X-RAY DIFFRACTION100
4.4879-5.13670.16871350.12721287X-RAY DIFFRACTION100
5.1367-6.46930.22091450.14791317X-RAY DIFFRACTION100
6.4693-48.55140.20161430.14691382X-RAY DIFFRACTION100

+
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