[English] 日本語
Yorodumi
- PDB-4fnm: The alpha-esterase-7 carboxylesterase, E3, from the blowfly Lucil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fnm
TitleThe alpha-esterase-7 carboxylesterase, E3, from the blowfly Lucilia cuprina
ComponentsE3 alpha-esterase-7 carboxylesterase
KeywordsHYDROLASE / alpha/beta hydrolase fold / carboxylesterase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity
Similarity search - Function
Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIETHYL HYDROGEN PHOSPHATE / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsJackson, C.J. / Liu, J.-W. / Carr, P.D. / Younis, F. / Pandey, G. / Coppin, C. / Meirelles, T. / Ollis, D.L. / Tawfik, D.S. / Weik, M. / Oakeshott, J.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure and function of an insect alpha-carboxylesterase ( alpha Esterase7) associated with insecticide resistance.
Authors: Jackson, C.J. / Liu, J.W. / Carr, P.D. / Younus, F. / Coppin, C. / Meirelles, T. / Lethier, M. / Pandey, G. / Ollis, D.L. / Russell, R.J. / Weik, M. / Oakeshott, J.G.
History
DepositionJun 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 alpha-esterase-7 carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4962
Polymers65,3421
Non-polymers1541
Water9,602533
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E3 alpha-esterase-7 carboxylesterase
hetero molecules

A: E3 alpha-esterase-7 carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9914
Polymers130,6832
Non-polymers3082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2750 Å2
ΔGint1 kcal/mol
Surface area41930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.650, 102.740, 226.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein E3 alpha-esterase-7 carboxylesterase


Mass: 65341.570 Da / Num. of mol.: 1 / Mutation: M364L, I419F, A472T, I505T, K530E, D554G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lucilia cuprina (Australian sheep blowfly)
Strain: LS2 / Gene: LcaE7 / Plasmid: pETMCSIII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q25252
#2: Chemical ChemComp-DPF / DIETHYL HYDROGEN PHOSPHATE


Mass: 154.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 100mM PEGMME 2K pH 4.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.8266 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2010 / Details: channel cut si(111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 54952 / Num. obs: 54477 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 28.11 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.55

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FG5

4fg5
PDB Unreleased entry


Resolution: 1.804→42.465 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 18.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 2737 5.03 %RANDOM
Rwork0.1696 ---
obs0.1713 54447 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.057 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2403 Å20 Å2-0 Å2
2--1.777 Å20 Å2
3----3.0173 Å2
Refine analyzeLuzzati coordinate error obs: 0.1786 Å
Refinement stepCycle: LAST / Resolution: 1.804→42.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 8 533 5085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064674
X-RAY DIFFRACTIONf_angle_d1.0376335
X-RAY DIFFRACTIONf_dihedral_angle_d14.7521737
X-RAY DIFFRACTIONf_chiral_restr0.074679
X-RAY DIFFRACTIONf_plane_restr0.005818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8043-1.83550.21861200.21542501X-RAY DIFFRACTION97
1.8355-1.86880.23851380.20332530X-RAY DIFFRACTION99
1.8688-1.90480.26471430.21062542X-RAY DIFFRACTION99
1.9048-1.94370.22351480.20532533X-RAY DIFFRACTION99
1.9437-1.98590.23061310.19512559X-RAY DIFFRACTION99
1.9859-2.03210.2721190.19352583X-RAY DIFFRACTION99
2.0321-2.08290.21821290.18732550X-RAY DIFFRACTION99
2.0829-2.13930.22541400.17542567X-RAY DIFFRACTION99
2.1393-2.20220.20661420.16882604X-RAY DIFFRACTION99
2.2022-2.27330.21441080.17562547X-RAY DIFFRACTION99
2.2733-2.35450.1871360.17282580X-RAY DIFFRACTION99
2.3545-2.44880.22421600.17622543X-RAY DIFFRACTION99
2.4488-2.56020.24341430.17922595X-RAY DIFFRACTION100
2.5602-2.69520.22381580.17742572X-RAY DIFFRACTION100
2.6952-2.8640.18821450.17032619X-RAY DIFFRACTION100
2.864-3.08510.2081390.17092562X-RAY DIFFRACTION100
3.0851-3.39540.19141320.16052661X-RAY DIFFRACTION100
3.3954-3.88650.17961300.1472621X-RAY DIFFRACTION100
3.8865-4.89540.16131370.14472668X-RAY DIFFRACTION100
4.8954-42.47720.19861390.1622773X-RAY DIFFRACTION99

+
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