[English] 日本語
Yorodumi
- PDB-1gce: STRUCTURE OF THE BETA-LACTAMASE OF ENTEROBACTER CLOACAE GC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gce
TitleSTRUCTURE OF THE BETA-LACTAMASE OF ENTEROBACTER CLOACAE GC1
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAM HYDROLASE / CEPHALOSPORINASE / DRUG DESIGN / EXTENDED-SPECTRUM BETA- LACTAMASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCrichlow, G.V. / Kuzin, A.P. / Nukaga, M. / Sawai, T. / Knox, J.R.
CitationJournal: Biochemistry / Year: 1999
Title: Structure of the extended-spectrum class C beta-lactamase of Enterobacter cloacae GC1, a natural mutant with a tandem tripeptide insertion.
Authors: Crichlow, G.V. / Kuzin, A.P. / Nukaga, M. / Mayama, K. / Sawai, T. / Knox, J.R.
History
DepositionMay 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)39,6091
Polymers39,6091
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.975, 69.514, 63.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21A-538-

HOH

31A-625-

HOH

-
Components

#1: Protein BETA-LACTAMASE / CEPHALOSPORINASE


Mass: 39609.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: GC1 / Cellular location: PERIPLASM / Plasmid: PTTQ18K-GC1 / Gene (production host): BLAC / Production host: Escherichia coli (E. coli) / Strain (production host): AS226-51 / References: UniProt: P05364, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.16 Å3/Da / Density % sol: 43 %
Description: PH GIVEN IS THAT OF A SOLUTION SIMILAR TO THE RESERVOIR SOLUION. THE PH FALLS IN THE RANGE OF 4 - 6.
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: VAPOR DIFFUSION, WITH 6.7 OR 8.0 MG/ML PROTEIN IN 5-7.5% PEG8000, 20-25MM POTASSIUM PHOSPHATE (MONOBASIC), OVER 12.5 OR 15% PEG8000, 50MM POTASSIUM PHOSPHATE (MONOBASIC) RESERVOIR AT ROOM ...Details: VAPOR DIFFUSION, WITH 6.7 OR 8.0 MG/ML PROTEIN IN 5-7.5% PEG8000, 20-25MM POTASSIUM PHOSPHATE (MONOBASIC), OVER 12.5 OR 15% PEG8000, 50MM POTASSIUM PHOSPHATE (MONOBASIC) RESERVOIR AT ROOM TEMPERATURE., temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113.4 mg/mlprotein1drop
212.5-15 %PEG80001reservoir
30.05-0.1 M1reservoirKH2PO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC / Detector: CCD / Date: Aug 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.8→99 Å / Num. obs: 31187 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 5 / Rsym value: 0.142 / % possible all: 80
Reflection
*PLUS
% possible obs: 96 % / Num. measured all: 122470
Reflection shell
*PLUS
% possible obs: 80 % / Num. unique obs: 2568 / Num. measured obs: 4591 / Mean I/σ(I) obs: 5.1

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BLT

2blt
PDB Unreleased entry


Resolution: 1.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: AFTER FINAL REFINEMENT, ONE WATER MOLECULE WAS DELETED FROM MODEL DUE TO B- FACTOR MORE THAN 55. AVG. B GIVEN REFLECTS STRUCTURE INCLUDING PROTEIN AND ONLY 235 WATER MOLECULES. THE FINAL ...Details: AFTER FINAL REFINEMENT, ONE WATER MOLECULE WAS DELETED FROM MODEL DUE TO B- FACTOR MORE THAN 55. AVG. B GIVEN REFLECTS STRUCTURE INCLUDING PROTEIN AND ONLY 235 WATER MOLECULES. THE FINAL ELECTRON DENSITY MAP CLEARLY SHOWS THAT NZ OF LYS67 IS COVALENTLY CROSSLINKED TO CE1 OF TYR150 VIA A BRIDGING (UNMODELED) ATOM, POSSIBLY NITROGEN. THIS UNUSUAL LINKAGE MIGHT HAVE DERIVED FROM THE AZIDE PRESENT IN THE LOW PH BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1502 5 %RANDOM
Rwork0.2018 ---
obs-30206 94.2 %-
Displacement parametersBiso mean: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 0 235 3008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.405
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.249
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2626 190 6 %
Rwork0.2482 2965 -
obs--79.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PROTEIN_REP.PARAMTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.249

+
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