[English] 日本語
Yorodumi
- PDB-5v3a: Novel Structural Insights into GDP-Mediated Regulation of Acyl-Co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v3a
TitleNovel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases
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 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
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
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
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,94712
Polymers73,1044
Non-polymers4,8438
Water10,016556
1
A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules

A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules

A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,92018
Polymers109,6566
Non-polymers7,26412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_456z-1,x,y+11
crystal symmetry operation9_546y,z-1,x+11
Buried area32380 Å2
ΔGint-159 kcal/mol
Surface area34630 Å2
MethodPISA
2
C: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)116,92018
Polymers109,6566
Non-polymers7,26412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area32400 Å2
ΔGint-168 kcal/mol
Surface area35560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.470, 152.470, 152.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-392-

HOH

21C-429-

HOH

-
Components

#1: Protein
Acyl-CoA hydrolase / Acyl-CoA thioesterase


Mass: 18275.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: A6L27_07605, ERS514410_00397, ERS514534_01643, ERS514708_01580, ERS514851_00814
Plasmid: pMCSG21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0Y5D4F5, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 4.04 Å3/Da / Density % sol: 69.54 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8.5
Details: 100mM Tris pH8.5, 2M ammonium Phosphate, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
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: Aug 24, 2012
RadiationMonochromator: silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→38.1 Å / Num. obs: 79600 / % possible obs: 100 % / Redundancy: 43 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 18.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 42 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 7831 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.979 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 4009 5.04 %
Rwork0.1809 --
obs0.1821 79577 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→36.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 304 556 5700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075248
X-RAY DIFFRACTIONf_angle_d1.2097140
X-RAY DIFFRACTIONf_dihedral_angle_d17.3461924
X-RAY DIFFRACTIONf_chiral_restr0.048792
X-RAY DIFFRACTIONf_plane_restr0.005876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.02370.28611390.242571X-RAY DIFFRACTION100
2.0237-2.04830.27831160.23352615X-RAY DIFFRACTION100
2.0483-2.07430.25671620.23562559X-RAY DIFFRACTION100
2.0743-2.10160.26461440.21832576X-RAY DIFFRACTION100
2.1016-2.13030.22581490.21292592X-RAY DIFFRACTION100
2.1303-2.16080.23031370.20742574X-RAY DIFFRACTION100
2.1608-2.1930.22361380.20292574X-RAY DIFFRACTION100
2.193-2.22730.24181130.19812607X-RAY DIFFRACTION100
2.2273-2.26380.20181280.19162613X-RAY DIFFRACTION100
2.2638-2.30280.1871340.18842603X-RAY DIFFRACTION100
2.3028-2.34470.20231360.18692597X-RAY DIFFRACTION100
2.3447-2.38980.25041430.19382535X-RAY DIFFRACTION100
2.3898-2.43860.24011590.19412566X-RAY DIFFRACTION100
2.4386-2.49160.21291340.18962649X-RAY DIFFRACTION100
2.4916-2.54950.20351310.1812574X-RAY DIFFRACTION100
2.5495-2.61330.221330.18432579X-RAY DIFFRACTION100
2.6133-2.68390.23681500.19272599X-RAY DIFFRACTION100
2.6839-2.76280.20331330.18172606X-RAY DIFFRACTION100
2.7628-2.8520.22581360.18772606X-RAY DIFFRACTION100
2.852-2.95390.24731250.17982635X-RAY DIFFRACTION100
2.9539-3.07210.21131510.17532590X-RAY DIFFRACTION100
3.0721-3.21180.18151620.182569X-RAY DIFFRACTION100
3.2118-3.38110.21131330.16942640X-RAY DIFFRACTION100
3.3811-3.59270.19781250.16872625X-RAY DIFFRACTION100
3.5927-3.86990.17311110.16292650X-RAY DIFFRACTION100
3.8699-4.25880.16981420.15682639X-RAY DIFFRACTION100
4.2588-4.87390.14831330.14812644X-RAY DIFFRACTION100
4.8739-6.1360.20121530.1832655X-RAY DIFFRACTION100
6.136-36.98570.19391590.1892726X-RAY DIFFRACTION99

+
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