[English] 日本語
Yorodumi
- PDB-1l7r: Tyr44Phe Mutant of Bacterial Cocaine Esterase cocE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l7r
TitleTyr44Phe Mutant of Bacterial Cocaine Esterase cocE
Componentscocaine esterase
KeywordsHYDROLASE / Bacterial cocaine esterase. Mutant of oxyanion hole. Hydrolase.
Function / homology
Function and homology information


cocaine esterase / cocaine catabolic process / dipeptidyl-peptidase activity / carboxylic ester hydrolase activity / cytoplasm
Similarity search - Function
alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / : / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like ...alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / : / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhodococcus sp. MB1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsTurner, J.M. / Larsen, N.A. / Basran, A. / Barbas III, C.F. / Bruce, N.C. / Wilson, I.A. / Lerner, R.A.
CitationJournal: Biochemistry / Year: 2002
Title: Biochemical characterization and structural analysis of a highly proficient cocaine esterase.
Authors: Turner, J.M. / Larsen, N.A. / Basran, A. / Barbas III, C.F. / Bruce, N.C. / Wilson, I.A. / Lerner, R.A.
History
DepositionMar 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cocaine esterase


Theoretical massNumber of molelcules
Total (without water)62,1671
Polymers62,1671
Non-polymers00
Water10,665592
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.193, 106.193, 220.872
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein cocaine esterase / cocE


Mass: 62167.352 Da / Num. of mol.: 1 / Mutation: Y44F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. MB1 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L9D7, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10mM Tris, 25mM NaCl, 1.4-1.6M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Method: microdialysis / Details: Larsen, N.A., (2002) Nature Struct. Biol., 9, 17.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris11pH7.5
225 mM11NaCl
310 mMdithiothreitol11
440 mg/mlprotein11
51.5-1.8 Mammonium sulfate12

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. all: 91569 / Num. obs: 91569 / % possible obs: 97.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.8 / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.8 / % possible all: 74.4
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 6.3 %
Reflection shell
*PLUS
% possible obs: 74.4 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JU4

1ju4


Resolution: 1.64→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.21 4578 RANDOM
Rwork0.19 --
all0.19 91569 -
obs0.19 91569 -
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 0 592 4962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

+
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