[English] 日本語
Yorodumi
- PDB-1o7e: Crystal structure of the class A beta-lactamse L2 from Stenotroph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o7e
TitleCrystal structure of the class A beta-lactamse L2 from Stenotrophomonas maltophilia at 1.51 angstrom
ComponentsL2 BETA LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE / CLASS A / L2
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
: / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...: / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTENOTROPHOMONAS MALTOPHILIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsPernot, L. / Petrella, S. / Sougakoff, W.
CitationJournal: To be Published
Title: Role of the Disulfide Bridge Cys69-Cys238 in Class a B-Lactamases : A Structural and Biochemical Investigation on the B-Lactamase L2 from Stenotrophomonas Maltophilia
Authors: Petrella, S. / Pernot, L. / Lascoux, D. / Forest, E. / Jarlier, V. / Sougakoff, W.
History
DepositionNov 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L2 BETA LACTAMASE
B: L2 BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,85318
Polymers58,3282
Non-polymers1,52516
Water13,205733
1
A: L2 BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9299
Polymers29,1641
Non-polymers7658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: L2 BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9259
Polymers29,1641
Non-polymers7618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.216, 133.216, 93.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.885043, -0.448562, 0.124462), (-0.452213, 0.765016, -0.458535), (0.110466, -0.462107, -0.879917)
Vector: 202.3484, 77.063, 97.7365)

-
Components

#1: Protein L2 BETA LACTAMASE


Mass: 29164.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STENOTROPHOMONAS MALTOPHILIA (bacteria)
Strain: 405 / Plasmid: PET29-(A+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RBQ1, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE L2 MATURE PROTEIN STARTS AT RESIDUE 28 THERE ARE NO RESIDUES NUMBERED 58 AND 239

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.23 %
Crystal growpH: 6.5
Details: AMMONIUM SULFATE 1.5M, SODIUM CACODYLATE 0.1M PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.948
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2001
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.51→23.9 Å / Num. obs: 131717 / % possible obs: 99.4 % / Observed criterion σ(I): 2.5 / Redundancy: 4.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.7
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9 / % possible all: 96

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE STARTING MODEL USED WAS THE ONE OF L2 AT 1.85 ANGSTROM, PDB ENTRY 1N4O

1n4o


Resolution: 1.51→23.92 Å / SU B: 0.9034 / SU ML: 0.0346 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.184 5238 4 %RANDOM
Rwork0.163 ---
obs0.17 131390 99.6 %-
Displacement parametersBiso mean: 13.9 Å2
Refinement stepCycle: LAST / Resolution: 1.51→23.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 83 733 4826

+
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