[English] 日本語
Yorodumi
- PDB-5d7b: Trigonal Crystal Structure of an acetylester hydrolase from Coryn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d7b
TitleTrigonal Crystal Structure of an acetylester hydrolase from Corynebacterium glutamicum
ComponentsHomoserine O-acetyltransferase
KeywordsHYDROLASE / Acetylester hydrolase / Alpha/Beta-Hydrolase
Function / homology
Function and homology information


homoserine O-acetyltransferase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / biosynthetic process / hydrolase activity
Similarity search - Function
Homoserine/serine acetyltransferase MetX-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable esterase Cgl0839
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNiefind, K. / Toelzer, C. / Pal, S. / Altenbuchner, J. / Watzlawick, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 635 Germany
CitationJournal: Febs Lett. / Year: 2016
Title: A novel esterase subfamily with alpha / beta-hydrolase fold suggested by structures of two bacterial enzymes homologous to l-homoserine O-acetyl transferases.
Authors: Tolzer, C. / Pal, S. / Watzlawick, H. / Altenbuchner, J. / Niefind, K.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,12217
Polymers77,7402
Non-polymers1,38115
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-21 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.393, 143.393, 197.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:349 )
211chain 'B' and (resseq 1:349 )

-
Components

#1: Protein Homoserine O-acetyltransferase / / Acetyl ester hydrolase


Mass: 38870.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg0961, Cgl0839 / Plasmid: pHWG771 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q8NS43, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, homoserine O-acetyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 7.52 Å3/Da / Density % sol: 83.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir: 25.5 %(w/v) polyethylenglycol 4000, 15 %(v/v) glycerol, 0.17 M Lithium sulfate, 85 mM Tris/HCl, pH 8.5 Drop: 0.4 microliter reservoir solution plut 0.8 microliter protein solution ...Details: Reservoir: 25.5 %(w/v) polyethylenglycol 4000, 15 %(v/v) glycerol, 0.17 M Lithium sulfate, 85 mM Tris/HCl, pH 8.5 Drop: 0.4 microliter reservoir solution plut 0.8 microliter protein solution with 5 mg/ml protein concentration

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.2→48.6 Å / Num. obs: 39336 / % possible obs: 99.93 % / Redundancy: 9.5 % / Rsym value: 0.245 / Net I/σ(I): 24.66
Reflection shellResolution: 3.2→3.314 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.66 / % possible all: 99.95

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B61

2b61


Resolution: 3.2→48.529 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1120 2.85 %Random selection
Rwork0.1868 ---
obs0.1872 39329 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→48.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 90 17 5591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025726
X-RAY DIFFRACTIONf_angle_d0.6037758
X-RAY DIFFRACTIONf_dihedral_angle_d11.5822050
X-RAY DIFFRACTIONf_chiral_restr0.021822
X-RAY DIFFRACTIONf_plane_restr0.0031016
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2753X-RAY DIFFRACTIONPOSITIONAL
12B2753X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.34570.2651500.26764707X-RAY DIFFRACTION100
3.3457-3.5220.27191410.23554681X-RAY DIFFRACTION100
3.522-3.74260.221420.21784725X-RAY DIFFRACTION100
3.7426-4.03140.18721410.18894738X-RAY DIFFRACTION100
4.0314-4.43690.18391300.15854752X-RAY DIFFRACTION100
4.4369-5.07830.15731390.15154791X-RAY DIFFRACTION100
5.0783-6.39580.19641450.17964806X-RAY DIFFRACTION100
6.3958-48.53490.20371320.18675009X-RAY DIFFRACTION100
Refinement TLS params.

L12: -0.8488 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.75740.54862.1951-0.74241.71860.26340.1492-0.3007-0.0257-0.08740.26270.29430.2266-0.14280.8890.0888-0.01560.3014-0.11830.593376.3272-12.930749.4163
21.82290.5732.3467-1.07832.00620.3170.35-0.4316-0.4947-0.16090.58150.1506-0.233-0.12350.96220.2328-0.1990.531-0.17980.815252.19285.284923.5326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

+
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