[English] 日本語
Yorodumi
- PDB-5egl: The structural and biochemical characterization of acyl-coa hydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5egl
TitleThe structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus in complex with Butyryl Coenzyme A, Coenzyme A, and Coenzyme A disulfide
ComponentsAcyl CoA Hydrolase
KeywordsHYDROLASE / Acyl CoA thioesterase / Staphylococcus aureus / Coenzyme A / Hotdog thioesterase
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic process / fatty acid catabolic process / 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
Chem-5NG / Butyryl Coenzyme A / COENZYME A / HotDog ACOT-type domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhandokar, Y.B. / Srivastava, P.S. / Forwood, J.K.
CitationJournal: To Be Published
Title: The structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus
Authors: Khandokar, Y.B. / Srivastava, P.S. / Forwood, J.K.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyl CoA Hydrolase
B: Acyl CoA Hydrolase
C: Acyl CoA Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1166
Polymers59,9783
Non-polymers3,1383
Water3,963220
1
A: Acyl CoA Hydrolase
B: Acyl CoA Hydrolase
C: Acyl CoA Hydrolase
hetero molecules

A: Acyl CoA Hydrolase
B: Acyl CoA Hydrolase
C: Acyl CoA Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,23212
Polymers119,9566
Non-polymers6,2766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area20450 Å2
ΔGint-120 kcal/mol
Surface area40170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.260, 142.260, 163.892
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-380-

HOH

-
Components

#1: Protein Acyl CoA Hydrolase


Mass: 19992.623 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV1878 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS / References: UniProt: A0A0H3K033
#2: Chemical ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)


Mass: 837.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O17P3S
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-5NG / [[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate / CoA-disulfide


Mass: 1533.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H70N14O32P6S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 4M Sodium formate

-
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: Oct 7, 2014
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: 2.1→39.84 Å / Num. obs: 57467 / % possible obs: 99.99 % / Redundancy: 2 % / Rmerge(I) obs: 0.02717 / Net I/σ(I): 13.83
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.23 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_1894refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCP

4ncp


Resolution: 2.1→39.835 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 2939 5.11 %
Rwork0.2125 --
obs0.2142 57459 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 197 220 4312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064181
X-RAY DIFFRACTIONf_angle_d1.1125682
X-RAY DIFFRACTIONf_dihedral_angle_d15.1811524
X-RAY DIFFRACTIONf_chiral_restr0.041619
X-RAY DIFFRACTIONf_plane_restr0.005706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13440.29511110.27542573X-RAY DIFFRACTION100
2.1344-2.17120.34991420.27332547X-RAY DIFFRACTION100
2.1712-2.21070.27811380.25822554X-RAY DIFFRACTION100
2.2107-2.25320.25771260.24942573X-RAY DIFFRACTION100
2.2532-2.29920.28491570.24662539X-RAY DIFFRACTION100
2.2992-2.34920.30151510.24352536X-RAY DIFFRACTION100
2.3492-2.40390.27941500.24092542X-RAY DIFFRACTION100
2.4039-2.4640.291460.23792559X-RAY DIFFRACTION100
2.464-2.53060.29271340.24392564X-RAY DIFFRACTION100
2.5306-2.6050.28971370.24522564X-RAY DIFFRACTION100
2.605-2.68910.27521390.23942583X-RAY DIFFRACTION100
2.6891-2.78520.26371200.24462610X-RAY DIFFRACTION100
2.7852-2.89670.26291530.24442571X-RAY DIFFRACTION100
2.8967-3.02850.27921370.24692581X-RAY DIFFRACTION100
3.0285-3.18810.27781370.23532595X-RAY DIFFRACTION100
3.1881-3.38770.26051510.22062601X-RAY DIFFRACTION100
3.3877-3.64910.23331330.20682617X-RAY DIFFRACTION100
3.6491-4.0160.23321340.18632631X-RAY DIFFRACTION100
4.016-4.59640.18631440.16022646X-RAY DIFFRACTION100
4.5964-5.78810.1841370.17222704X-RAY DIFFRACTION100
5.7881-39.84250.24351620.20742830X-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