[English] 日本語
Yorodumi
- PDB-3doh: Crystal Structure of a Thermostable Esterase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3doh
TitleCrystal Structure of a Thermostable Esterase
Componentsesterase
KeywordsHYDROLASE / alpha-beta Hydrolase / beta sheet
Function / homology
Function and homology information


Immunoglobulin-like - #2180 / Esterase, Ig-like N-terminal / Esterase Ig-like N-terminal domain / : / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulin-like / Sandwich ...Immunoglobulin-like - #2180 / Esterase, Ig-like N-terminal / Esterase Ig-like N-terminal domain / : / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsLevisson, M. / Sun, L. / Hendriks, S. / Dijkstra, B.W. / Van der Oost, J. / Kengen, S.W.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain.
Authors: Levisson, M. / Sun, L. / Hendriks, S. / Swinkels, P. / Akveld, T. / Bultema, J.B. / Barendregt, A. / van den Heuvel, R.H.H. / Dijkstra, B.W. / van der Oost, J. / Kengen, S.W.M.
History
DepositionJul 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: esterase
B: esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,09612
Polymers86,1362
Non-polymers96110
Water2,810156
1
A: esterase
B: esterase
hetero molecules

A: esterase
B: esterase
hetero molecules

A: esterase
B: esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,28836
Polymers258,4076
Non-polymers2,88230
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
A: esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6447
Polymers43,0681
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4525
Polymers43,0681
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.157, 130.157, 306.184
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein esterase


Mass: 43067.750 Da / Num. of mol.: 2 / Fragment: residues 16-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0033 / Plasmid: pET-24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WXP0, carboxylesterase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 8000, 1M lithium sulphate monohydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0000, 0.9791, 0.9793, 0.9757
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2007 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.97931
40.97571
ReflectionResolution: 2.6→50 Å / Num. obs: 31079 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→19.96 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / SU B: 11.516 / SU ML: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.693 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26772 1506 5 %RANDOM
Rwork0.19655 ---
obs0.2002 28373 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 50 156 6188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226185
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.9648427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3045745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95324.476286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.566151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9161529
X-RAY DIFFRACTIONr_chiral_restr0.1350.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024719
X-RAY DIFFRACTIONr_nbd_refined0.2470.23016
X-RAY DIFFRACTIONr_nbtor_refined0.3290.24127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2323
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.210
X-RAY DIFFRACTIONr_mcbond_it0.9311.53841
X-RAY DIFFRACTIONr_mcangle_it1.63926111
X-RAY DIFFRACTIONr_scbond_it2.00732706
X-RAY DIFFRACTIONr_scangle_it3.2424.52316
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 98 -
Rwork0.312 2092 -
obs--98.47 %

+
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