[English] 日本語
Yorodumi
- PDB-1tht: STRUCTURE OF A MYRISTOYL-ACP-SPECIFIC THIOESTERASE FROM VIBRIO HARVEYI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tht
TitleSTRUCTURE OF A MYRISTOYL-ACP-SPECIFIC THIOESTERASE FROM VIBRIO HARVEYI
ComponentsTHIOESTERASE
KeywordsTHIOESTERASE
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / bioluminescence / fatty acid metabolic process
Similarity search - Function
Acyl transferase, LuxD / Acyl transferase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsLawson, D.M. / Derewenda, U. / Serre, L. / Ferri, S. / Szitter, R. / Wei, Y. / Meighen, E.A. / Derewenda, Z.S.
CitationJournal: Biochemistry / Year: 1994
Title: Structure of a myristoyl-ACP-specific thioesterase from Vibrio harveyi.
Authors: Lawson, D.M. / Derewenda, U. / Serre, L. / Ferri, S. / Szittner, R. / Wei, Y. / Meighen, E.A. / Derewenda, Z.S.
History
DepositionApr 19, 1994Processing site: BNL
Revision 1.0Jun 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE STRANDS OF S2 IN *SHEET* RECORDS BELOW BOTH BELONG TO THE CAP DOMAIN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOESTERASE
B: THIOESTERASE


Theoretical massNumber of molelcules
Total (without water)68,4852
Polymers68,4852
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.500, 83.800, 47.400
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHERE ARE TWO MOLECULES PER ASYMMETRIC UNIT.

-
Components

#1: Protein THIOESTERASE


Mass: 34242.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / References: UniProt: P05521
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Swenson, L., (1992) J.Mol. Biol, 227, 572.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
2100 mMpotassium phosphate1drop
320 %glycerol1drop
455 %satammonium sulfate1drop
5100 mMpotassium phosphate1drop
61 %PEG2001drop
755 %satammonium sulfate1reservoir
8100 mMpotassium phosphate1reservoir
91 %PEG2001reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2.06 Å / Num. obs: 36778 / % possible obs: 86 % / Observed criterion σ(I): 14.3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.09

-
Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 1 /
RfactorNum. reflection
obs0.227 36771
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 0 55 4649
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0580.058
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0770.077
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.3883.388
X-RAY DIFFRACTIONp_mcangle_it5.1245.124
X-RAY DIFFRACTIONp_scbond_it4.0254.025
X-RAY DIFFRACTIONp_scangle_it6.0246.024
X-RAY DIFFRACTIONp_plane_restr0.0280.028
X-RAY DIFFRACTIONp_chiral_restr0.1370.137
X-RAY DIFFRACTIONp_singtor_nbd0.1740.174
X-RAY DIFFRACTIONp_multtor_nbd0.260.26
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1160.116
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.7944.794
X-RAY DIFFRACTIONp_staggered_tor18.32418.324
X-RAY DIFFRACTIONp_orthonormal_tor32.10732.107
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

+
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