[English] 日本語
Yorodumi
- PDB-1ci9: DFP-INHIBITED ESTERASE ESTB FROM BURKHOLDERIA GLADIOLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ci9
TitleDFP-INHIBITED ESTERASE ESTB FROM BURKHOLDERIA GLADIOLI
ComponentsPROTEIN (CARBOXYLESTERASE)
KeywordsHYDROLASE / CABOXYLESTERASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity / cytoplasm
Similarity search - Function
Beta-lactamase-related / Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIISOPROPYL PHOSPHONATE / Esterase EstB
Similarity search - Component
Biological speciesBurkholderia gladioli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsWagner, U.G. / Petersen, E.I. / Schwab, H. / Kratky, C.
Citation
Journal: Protein Sci. / Year: 2002
Title: EstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity
Authors: Wagner, U.G. / Petersen, E.I. / Schwab, H. / Kratky, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and preliminary X-ray diffraction studies of the Pseudomonas marginata esterase EstB.
Authors: Wagner, U.G. / Solkner, B. / Petersen, E.I. / Schlacher, A. / Schwab, H. / Kratky, C.
History
DepositionApr 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 27, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / struct_conn
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 27, 2023Group: 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
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / refine
Item: _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model
Remark 999SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE IN SEQUENCE DATABASE

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (CARBOXYLESTERASE)
B: PROTEIN (CARBOXYLESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8354
Polymers83,5022
Non-polymers3322
Water10,287571
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.444, 83.444, 194.576
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.504007, -0.863289, -0.026608), (-0.858029, 0.496936, 0.12977), (-0.098807, 0.088236, -0.991187)
Vector: 11.332, -13.112, 220.61501)

-
Components

#1: Protein PROTEIN (CARBOXYLESTERASE) / ESTB


Mass: 41751.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia gladioli (bacteria) / Cellular location: INTRACELLULAR / Gene: ESTB / Plasmid: PMS470(DELTA)8 / Cellular location (production host): INTRACELLULAR / Production host: Escherichia coli (E. coli) / Strain (production host): E.COLI K12 / References: UniProt: Q9KX40, carboxylesterase
#2: Chemical ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.4 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5
Details: 10% PEG 4000, 10% 2-PROPANOL, 0.05M NA HEPES BUFFER (PH=7.5), pH 7.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MHEPES1reservoirpH7.5
210 %2-propanol1reservoir
320 20PEG40001reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 69158 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.024
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rsym value: 0.118 / % possible all: 96.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / % possible obs: 94 % / Redundancy: 5.2 % / Num. measured all: 235197
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 97 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.108

-
Processing

Software
NameVersionClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→15 Å / Num. parameters: 25111 / Num. restraintsaints: 23545 / Cross valid method: AFTER SOLUTION / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 3515 5.4 %RANDOM
Rwork0.1759 ---
all-65643 --
obs-65643 95 %-
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 20 571 6261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.027
X-RAY DIFFRACTIONs_angle_d1.89
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELX / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Rfactor all: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.89
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

+
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