[English] 日本語
Yorodumi
- PDB-8z5l: Crystal structure of metallo-beta-lactamse, IMP-1, complexed with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z5l
TitleCrystal structure of metallo-beta-lactamse, IMP-1, complexed with a quinolinone-based inhibitor
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-lactamase inhibitor / ANTIBIOTIC / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKamo, T. / Kuroda, K. / Nimura, S. / Guo, Y. / Kondo, S. / Nukaga, M. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04462 Japan
CitationJournal: Biochemistry / Year: 2024
Title: Development of Inhibitory Compounds for Metallo-beta-lactamase through Computational Design and Crystallographic Analysis.
Authors: Kamo, T. / Kuroda, K. / Nimura, S. / Guo, Y. / Kondo, S. / Nukaga, M. / Hoshino, T.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 8, 2024ID: 8Y0S
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
C: Metallo-beta-lactamase type 2
D: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,40318
Polymers102,7414
Non-polymers1,66214
Water1,27971
1
A: Metallo-beta-lactamase type 2
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 25.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)25,8824
Polymers25,6851
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


  • defined by author
  • 26.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)26,3205
Polymers25,6851
Non-polymers6354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Metallo-beta-lactamase type 2
hetero molecules


  • defined by author
  • 26.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)26,3205
Polymers25,6851
Non-polymers6354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Metallo-beta-lactamase type 2
hetero molecules


  • defined by author
  • 25.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)25,8824
Polymers25,6851
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.607, 77.619, 259.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / BLA-IMP / IMP-1 / Beta-lactamase type II / Metallo-beta-lactamase type II


Mass: 25685.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: PET48B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3)PLYS / References: UniProt: P52699, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1LXO / 3-[2-azanyl-5-[2-cyclohexylethyl-[3-(4-methylphenoxy)propyl]amino]phenyl]propanoic acid


Mass: 438.602 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H38N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM HEPES, 15%(W/V) PEG 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→45.52 Å / Num. obs: 29377 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.073 / Rrim(I) all: 0.176 / Χ2: 1.07 / Net I/σ(I): 10.5 / Num. measured all: 180450
Reflection shellResolution: 2.65→2.78 Å / % possible obs: 98.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 1.083 / Num. measured all: 23066 / Num. unique obs: 3809 / CC1/2: 0.705 / Rpim(I) all: 0.483 / Rrim(I) all: 1.189 / Χ2: 0.96 / Net I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→43.3 Å / SU ML: 0.44 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 33.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 1995 6.83 %
Rwork0.2097 --
obs0.215 29209 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7052 0 76 71 7199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.149
X-RAY DIFFRACTIONf_dihedral_angle_d7.736984
X-RAY DIFFRACTIONf_chiral_restr0.0581088
X-RAY DIFFRACTIONf_plane_restr0.0091242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.44741380.35841876X-RAY DIFFRACTION97
2.72-2.790.42031410.31651914X-RAY DIFFRACTION99
2.79-2.870.42751420.30071946X-RAY DIFFRACTION100
2.87-2.970.35491390.28411897X-RAY DIFFRACTION100
2.97-3.070.33331400.28881923X-RAY DIFFRACTION99
3.07-3.20.39461420.24241924X-RAY DIFFRACTION100
3.2-3.340.29321400.2361910X-RAY DIFFRACTION99
3.34-3.520.32481440.221969X-RAY DIFFRACTION100
3.52-3.740.27661420.2151937X-RAY DIFFRACTION99
3.74-4.030.27231420.20271933X-RAY DIFFRACTION99
4.03-4.430.27081440.1781954X-RAY DIFFRACTION99
4.43-5.070.24611430.1631957X-RAY DIFFRACTION99
5.07-6.380.25721460.1852001X-RAY DIFFRACTION99
6.39-43.30.22041520.16622073X-RAY DIFFRACTION96

+
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