[English] 日本語
Yorodumi
- PDB-5t02: Structural characterisation of mutant Asp39Ala of thioesterase (N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t02
TitleStructural characterisation of mutant Asp39Ala of thioesterase (NmACH) from Neisseria meningitidis
ComponentsAcyl-CoA hydrolase
KeywordsHYDROLASE / Thioesterase / Nisseria meningitidis / 4HBT / Acyl-CoA thioesterase / Coenzyme A / GDP
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / GUANOSINE-5'-DIPHOSPHATE / Acyl-CoA hydrolase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase.
Authors: Khandokar, Y.B. / Srivastava, P. / Cowieson, N. / Sarker, S. / Aragao, D. / Das, S. / Smith, K.M. / Raidal, S.R. / Forwood, J.K.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: 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: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
E: Acyl-CoA hydrolase
F: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,28924
Polymers107,8126
Non-polymers7,47718
Water00
1
B: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
F: Acyl-CoA hydrolase
hetero molecules

D: Acyl-CoA hydrolase
E: Acyl-CoA hydrolase
hetero molecules

A: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,28924
Polymers107,8126
Non-polymers7,47718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation3_455-x+y-1,-x,z+2/31
Buried area29140 Å2
ΔGint-211 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.070, 226.070, 68.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Acyl-CoA hydrolase


Mass: 17968.611 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: ERS514298_01532, ERS514410_00397, ERS514534_01643, ERS514708_01580, ERS514851_00814
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: A0A0Y5D4F5, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.67 Å3/Da / Density % sol: 73.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.4 M ammonium phosphate monobasic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→39.79 Å / Num. obs: 49406 / % possible obs: 99.98 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.87
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IEN

4ien


Resolution: 2.8→39.789 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.73
RfactorNum. reflection% reflection
Rfree0.2121 2369 4.8 %
Rwork0.1733 --
obs0.1751 49344 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6945 0 462 0 7407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097551
X-RAY DIFFRACTIONf_angle_d1.26310292
X-RAY DIFFRACTIONf_dihedral_angle_d19.6572906
X-RAY DIFFRACTIONf_chiral_restr0.0471147
X-RAY DIFFRACTIONf_plane_restr0.0061252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.85730.2781310.24772765X-RAY DIFFRACTION100
2.8573-2.91940.28441430.23252701X-RAY DIFFRACTION100
2.9194-2.98730.26441390.21932768X-RAY DIFFRACTION100
2.9873-3.0620.25281260.2062731X-RAY DIFFRACTION100
3.062-3.14470.28721300.20742768X-RAY DIFFRACTION100
3.1447-3.23720.24281600.21082715X-RAY DIFFRACTION100
3.2372-3.34170.24211180.18672754X-RAY DIFFRACTION100
3.3417-3.4610.2511350.18822763X-RAY DIFFRACTION100
3.461-3.59950.21141420.18122744X-RAY DIFFRACTION100
3.5995-3.76320.21091480.16292752X-RAY DIFFRACTION100
3.7632-3.96150.21051350.16622753X-RAY DIFFRACTION100
3.9615-4.20940.16951390.15342762X-RAY DIFFRACTION100
4.2094-4.5340.1621580.13562759X-RAY DIFFRACTION100
4.534-4.98950.17211530.13282760X-RAY DIFFRACTION100
4.9895-5.70970.19391330.15132804X-RAY DIFFRACTION100
5.7097-7.18670.21141350.16862793X-RAY DIFFRACTION100
7.1867-39.79250.19711440.17362883X-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