[English] 日本語
Yorodumi
- PDB-1evq: THE CRYSTAL STRUCTURE OF THE THERMOPHILIC CARBOXYLESTERASE EST2 F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1evq
TitleTHE CRYSTAL STRUCTURE OF THE THERMOPHILIC CARBOXYLESTERASE EST2 FROM ALICYCLOBACILLUS ACIDOCALDARIUS
ComponentsSERINE HYDROLASE
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Hydrolase
Function and homology information
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsDe Simone, G. / Galdiero, S. / Manco, G. / Lang, D. / Rossi, M. / Pedone, C.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: A snapshot of a transition state analogue of a novel thermophilic esterase belonging to the subfamily of mammalian hormone-sensitive lipase.
Authors: De Simone, G. / Galdiero, S. / Manco, G. / Lang, D. / Rossi, M. / Pedone, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Diffraction Studies of the Carboxylesterase EST2 from Alicyclobacillus acidocaldarius
Authors: De Simone, G. / Manco, G. / Galdiero, S. / Lombardi, A. / Rossi, M. / Pavone, V.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: Crystal Structure of Brefeldin A Esterase, a Bacterial Homolog of the Mammalian Hormone-sensitive Lipase
Authors: Wei, Y. / Contreras, J.A. / Sheffield, P. / Osterlund, T. / Derewenda, U. / Kneusel, R.E. / Matern, U. / Holm, C. / Derewenda, Z.S.
History
DepositionApr 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8873
Polymers34,5271
Non-polymers3602
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.105, 79.105, 107.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer

-
Components

#1: Protein SERINE HYDROLASE /


Mass: 34526.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Plasmid: PT7-7SCII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIG1, carboxylesterase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 48.8 %
Description: Wavelength 0.9785 is the peak wavelength, 0.9786 is the inflection, and 0.9810 is remote.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 2% PEG 400, 100mM Hepes pH 7.8, 2M Ammonium Sulphate, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
pH: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMTris-HCl1drop
20.1 M1dropNaCl
32.5 mM1dropMgCl2
44 mg/mlprotein1drop
52 Mammonium sulfate1reservoir
6100 mMHEPES1reservoir
72 %PEG4001reservoir
81 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.9785, 0.9786, 0.9810
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 10, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.97861
30.9811
ReflectionResolution: 2.6→100 Å / Num. all: 203297 / Num. obs: 10886 / % possible obs: 99.4 % / Redundancy: 18 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 31
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.236 / Num. unique all: 1057 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 8.8

-
Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 515 5 %RANDOM
Rwork0.216 ---
all-10753 --
obs-10753 98 %-
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 22 78 2523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.6

+
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