[English] 日本語
Yorodumi
- PDB-4ubj: KINETIC CRYSTALLOGRAPHY OF ALPHA_E7-CARBOXYLESTERSE FROM LUCILLA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ubj
TitleKINETIC CRYSTALLOGRAPHY OF ALPHA_E7-CARBOXYLESTERSE FROM LUCILLA CUPRINA - ABSORBED X-RAY DOSE 5.55 MGy at 100K
ComponentsE3
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: 2.3 Å
AuthorsJackson, C.J. / Carr, P.D. / Weik, M. / Huber, T. / Meirelles, T. / Correy, G.
CitationJournal: Structure / Year: 2016
Title: Mapping the Accessible Conformational Landscape of an Insect Carboxylesterase Using Conformational Ensemble Analysis and Kinetic Crystallography
Authors: Correy, G.J. / Carr, P.D. / Meirelles, T. / Mabbitt, P.D. / Fraser, N.J. / Weik, M. / Jackson, C.J.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list / reflns_shell
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.Rmerge_I_obs
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6272
Polymers65,4731
Non-polymers1541
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint4 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.539, 101.073, 222.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-738-

HOH

-
Components

#1: Protein E3


Mass: 65472.773 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)
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.: 208 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 100MM PEG2000, 0.1M MES, PH 4.6, VAPOR DIFFUSION, TEMPERATURE 298K
PH range: 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→46.01 Å / Num. obs: 24832 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1639)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QWM

4qwm


Resolution: 2.3→46.006 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1262 5.09 %
Rwork0.1699 --
obs0.1732 24795 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 8 208 4775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084688
X-RAY DIFFRACTIONf_angle_d1.046341
X-RAY DIFFRACTIONf_dihedral_angle_d14.3171759
X-RAY DIFFRACTIONf_chiral_restr0.04677
X-RAY DIFFRACTIONf_plane_restr0.005817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.32671330.23642590X-RAY DIFFRACTION100
2.3921-2.5010.30761330.22232542X-RAY DIFFRACTION100
2.501-2.63280.34231300.20992612X-RAY DIFFRACTION100
2.6328-2.79770.23391480.19582590X-RAY DIFFRACTION100
2.7977-3.01370.281350.18822579X-RAY DIFFRACTION100
3.0137-3.31690.23541510.17572597X-RAY DIFFRACTION100
3.3169-3.79670.23271160.15942640X-RAY DIFFRACTION100
3.7967-4.78260.19511570.1432632X-RAY DIFFRACTION100
4.7826-46.01560.21011590.15572751X-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