[English] 日本語
Yorodumi
- PDB-7aw5: Crystal structure of OXA-48 beta-lactamase in the complex with th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aw5
TitleCrystal structure of OXA-48 beta-lactamase in the complex with the inhibitor ID3
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class D Beta-lactamase / OXA-48 / antibiotic / dimer
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-LKH / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPochetti, G. / Montanari, R. / Capelli, D. / Garofalo, B. / Ombrato, R.
CitationJournal: Pharmaceuticals / Year: 2021
Title: Discovery of Novel Chemical Series of OXA-48 beta-Lactamase Inhibitors by High-Throughput Screening.
Authors: Garofalo, B. / Prati, F. / Buonfiglio, R. / Coletta, I. / D'Atanasio, N. / Molteni, A. / Carettoni, D. / Wanke, V. / Pochetti, G. / Montanari, R. / Capelli, D. / Milanese, C. / Di Giorgio, F.P. / Ombrato, R.
History
DepositionNov 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9495
Polymers56,1962
Non-polymers7533
Water11,025612
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-9 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.470, 73.680, 124.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Beta-lactamase


Mass: 28097.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the Lysin 73 is caboxylated (KCX) / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-LKH / 4-[(~{E})-[3-(4-chlorophenyl)-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl]iminomethyl]benzoic acid


Mass: 358.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11ClN4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes, pH 7.5, 12% PEG8000, 8% 1-butanol, OXA-48 8.0-8.5 mg/ml, inhibitor/protein ratio 6.5:1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.65→51.67 Å / Num. obs: 80899 / % possible obs: 99.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.38 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.5
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 3950 / CC1/2: 0.916

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 1.65→51.667 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 2008 2.49 %
Rwork0.1763 78757 -
obs0.177 80765 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.84 Å2 / Biso mean: 21.26 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 1.65→51.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 49 630 4636
Biso mean--42.43 33.14 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094101
X-RAY DIFFRACTIONf_angle_d1.1565552
X-RAY DIFFRACTIONf_chiral_restr0.045577
X-RAY DIFFRACTIONf_plane_restr0.005714
X-RAY DIFFRACTIONf_dihedral_angle_d15.0351502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.69120.22651410.21525550100
1.6912-1.7370.19571350.19575528100
1.737-1.78810.24141470.1898552499
1.7881-1.84580.19211420.18045604100
1.8458-1.91180.21651440.18315571100
1.9118-1.98830.211450.18045574100
1.9883-2.07880.23461360.18775593100
2.0788-2.18840.1941420.18175588100
2.1884-2.32550.24861400.17895608100
2.3255-2.50510.24271460.1855626100
2.5051-2.75710.20561400.1865644100
2.7571-3.1560.20091470.18345684100
3.156-3.97610.20011480.16195715100
3.9761-100.18251550.15845948100

+
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