[English] 日本語
Yorodumi
- PDB-5eo4: Structural and biochemical characterization of the hypothetical p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eo4
TitleStructural and biochemical characterization of the hypothetical protein SAV2348 from Staphylococcus aureus.
Componentsthioesterase
KeywordsHYDROLASE / Thioesterases / hypothetical protein SAV2348 / staphylococcus aureus / coenzyme A
Function / homologyThioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Thioesterase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
CitationJournal: To Be Published
Title: Structural and biochemical characterization of the hypothetical protein SAV2348 from Staphylococcus aureus.
Authors: Khandokar, Y.B. / Srivastava, P. / Forwood, J.K.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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: thioesterase
B: thioesterase
C: thioesterase


Theoretical massNumber of molelcules
Total (without water)57,3553
Polymers57,3553
Non-polymers00
Water5,549308
1
A: thioesterase

A: thioesterase


Theoretical massNumber of molelcules
Total (without water)38,2372
Polymers38,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_357-x-2,y,-z+21
Buried area3470 Å2
ΔGint-9 kcal/mol
Surface area15050 Å2
MethodPISA
2
B: thioesterase
C: thioesterase


Theoretical massNumber of molelcules
Total (without water)38,2372
Polymers38,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-12 kcal/mol
Surface area14620 Å2
MethodPISA
3
A: thioesterase
B: thioesterase
C: thioesterase

A: thioesterase
B: thioesterase
C: thioesterase


Theoretical massNumber of molelcules
Total (without water)114,7116
Polymers114,7116
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_357-x-2,y,-z+21
Buried area13480 Å2
ΔGint-52 kcal/mol
Surface area41120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.070, 62.660, 149.357
Angle α, β, γ (deg.)90.00, 92.47, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein thioesterase


Mass: 19118.453 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: SAV2348 / Plasmid: pMCSG21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: A0A0H3JSY9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.2M ammonium tartrate dibasic pH6.2, 26% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48 Å / Num. obs: 39242 / % possible obs: 99.3 % / Redundancy: 2 % / Net I/σ(I): 11.91

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2→44.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 1917 4.9 %RANDOM
Rwork0.1802 ---
obs0.1823 37325 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 0 308 4135
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 152 -
Rwork0.176 2730 -
obs--99.76 %

+
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