[English] 日本語
Yorodumi
- PDB-1t82: Crystal Structure of the putative thioesterase from Shewanella on... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t82
TitleCrystal Structure of the putative thioesterase from Shewanella oneidensis, Northeast Structural Genomics Target SoR51
Componentshypothetical acetyltransferase
KeywordsTRANSFERASE / structural genomics / alpha-beta dimeric protein with a fold resembling a hotdog / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyThioesterase, putative / Putative thioesterase (yiiD_Cterm) / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / acyltransferase activity, transferring groups other than amino-acyl groups / Roll / Alpha Beta / Thioesterase domain protein YiiD
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsForouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the putative thioesterase from Shewanella oneidensis, Northeast Structural Genomics Target SoR51
Authors: Forouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical acetyltransferase
B: hypothetical acetyltransferase
C: hypothetical acetyltransferase
D: hypothetical acetyltransferase


Theoretical massNumber of molelcules
Total (without water)71,4064
Polymers71,4064
Non-polymers00
Water7,819434
1
A: hypothetical acetyltransferase
B: hypothetical acetyltransferase


Theoretical massNumber of molelcules
Total (without water)35,7032
Polymers35,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-19 kcal/mol
Surface area13060 Å2
MethodPISA
2
C: hypothetical acetyltransferase
D: hypothetical acetyltransferase


Theoretical massNumber of molelcules
Total (without water)35,7032
Polymers35,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-23 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.980, 49.669, 99.670
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
hypothetical acetyltransferase


Mass: 17851.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Plasmid: BL21(DE3)+Magic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8E989
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10mM Tris, 100mM NaCl, 5mM DTT. Reservoir solution: 20% PEG 3350, 200mM sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→29.81 Å / Num. all: 112723 / Num. obs: 107847 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.43 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.079 / Net I/σ(I): 21
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 9.73 / Num. unique all: 15130 / Rsym value: 0.171 / % possible all: 86.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVEphasing
CNSrefinement
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.81 Å
Isotropic thermal model: anisotropic and overall temperature factors
Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 10507 -random
Rwork0.194 ---
all-107847 --
obs-107847 92.9 %-
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-2.47 Å2
2--1.64 Å20 Å2
3----0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.05 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 0 434 4931
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.005
RfactorNum. reflection% reflection
Rfree0.221 10507 -
Rwork0.189 --
obs-15130 10.1 %

+
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