[English] 日本語
Yorodumi
- PDB-1jji: The Crystal Structure of a Hyper-thermophilic Carboxylesterase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jji
TitleThe Crystal Structure of a Hyper-thermophilic Carboxylesterase from the Archaeon Archaeoglobus fulgidus
ComponentsCarboxylesterase
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 / Carboxylesterase (EstA)
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDe Simone, G. / Menchise, V. / Manco, G. / Mandrich, L. / Sorrentino, N. / Lang, D. / Rossi, M. / Pedone, C.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The crystal structure of a hyper-thermophilic carboxylesterase from the archaeon Archaeoglobus fulgidus.
Authors: De Simone, G. / Menchise, V. / Manco, G. / Mandrich, L. / Sorrentino, N. / Lang, D. / Rossi, M. / Pedone, C.
#1: Journal: ARCH.BIOCHEM.BIOPHYS. / Year: 2000
Title: Cloning, Overexpression and Properties of a New Thermophilic and Termostable Esterase with Sequence Similarity to Hormone-Sensitive Lipase Subfamily from the archaeon Archaeoglobus fulgidus
Authors: Manco, G. / Giosue, E. / D'Auria, S. / Herman, P. / Carrea, G. / Rossi, M.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: A snapshot of the transition state 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.
History
DepositionJul 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_initial_refinement_model / struct_conn / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carboxylesterase
B: Carboxylesterase
C: Carboxylesterase
D: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0748
Polymers142,1214
Non-polymers9534
Water10,106561
1
A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7682
Polymers35,5301
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7682
Polymers35,5301
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7682
Polymers35,5301
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7682
Polymers35,5301
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
A: Carboxylesterase
B: Carboxylesterase
C: Carboxylesterase
D: Carboxylesterase
hetero molecules

A: Carboxylesterase
B: Carboxylesterase
C: Carboxylesterase
D: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,14816
Polymers284,2418
Non-polymers1,9068
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area23410 Å2
ΔGint-33 kcal/mol
Surface area85290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.050, 169.050, 104.544
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein
Carboxylesterase


Mass: 35530.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: PT7-7SCII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28558, carboxylesterase
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 3.03 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Peg 4000, Magnesium acetate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris-HCl1droppH8.3
22.5 mM1dropMgCl2
30.5 mMEDTA1drop
48 mg/mlprotein1drop
515 %(w/v)PEG40001reservoir
60.3 Mmagnesium acetate1reservoir
70.1 Msodium HEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 2000 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 84834 / Num. obs: 84834 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.7
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.94 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 920049
Reflection shell
*PLUS
% possible obs: 84.7 % / Rmerge(I) obs: 0.361

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EVQ

1evq


Resolution: 2.2→8 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4177 5 %random
Rwork0.203 ---
all-83680 --
obs-83680 99.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10032 0 56 561 10649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.45
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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