[English] 日本語
Yorodumi
- PDB-7u70: Crystal Structure of CTX-M-14 with compound 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u70
TitleCrystal Structure of CTX-M-14 with compound 2
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE inhibitor / beta-lactamase / tetrazole / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
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 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LW0 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsAkhtar, A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161762 United States
CitationJournal: To Be Published
Title: Probing the binding hot spots of KPC-2 carbapenemase using reversible tetrazole-based inhibitors
Authors: DeFrees, K. / Cambeis, E.M. / Chen, Y. / Renslo, A.R.
History
DepositionMar 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)56,6484
Polymers56,0012
Non-polymers6472
Water13,818767
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3242
Polymers28,0011
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3242
Polymers28,0011
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.250, 106.800, 47.730
Angle α, β, γ (deg.)90.000, 101.840, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-lactamase


Mass: 28000.547 Da / Num. of mol.: 2 / Fragment: UNP residues 23-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6UQI0, beta-lactamase
#2: Chemical ChemComp-LW0 / 3-fluoro-N-[(1R,3S)-3-(1H-tetrazol-5-yl)-2,3-dihydro-1H-inden-1-yl]benzamide


Mass: 323.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14FN5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.0 M potassium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→46.715 Å / Num. all: 92146 / Num. obs: 92146 / % possible obs: 97.2 % / Redundancy: 3.3 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Rsym value: 0.063 / Net I/av σ(I): 6.9 / Net I/σ(I): 11.4 / Num. measured all: 305381
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.36-1.433.20.2133.242330133160.1420.2580.2134.996.5
1.43-1.523.20.16439365122770.1060.1930.166.293.8
1.52-1.633.40.1275.341910122420.0810.1510.1277.999.4
1.63-1.763.30.1056.237667113040.0680.1260.1059.298.9
1.76-1.923.20.0797.832818102120.0520.0950.07911.297
1.92-2.153.30.0629.82931889850.040.0740.06214.693.8
2.15-2.483.60.05510.93002384100.0340.0650.05517.499.9
2.48-3.043.50.052112434570430.0330.0620.05218.999
3.04-4.33.20.04811.61668652850.0320.0580.0482195.9
4.3-46.7153.60.04412.81091930720.0270.0520.04422.5100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.36→46.715 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1711 2001 2.17 %
Rwork0.1507 90094 -
obs0.1512 92095 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.02 Å2 / Biso mean: 12.8037 Å2 / Biso min: 3.96 Å2
Refinement stepCycle: final / Resolution: 1.36→46.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 48 767 4713
Biso mean--12.5 24.12 -
Num. residues----522
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.36-1.3940.22241510.1824639997
1.394-1.43170.2041230.1697637996
1.4317-1.47380.22391400.1674585089
1.4738-1.52140.19441320.1573652599
1.5214-1.57580.17541570.1522657799
1.5758-1.63890.15071410.1484659099
1.6389-1.71350.18971470.1548650499
1.7135-1.80380.2081430.1602653898
1.8038-1.91680.1691470.1513638396
1.9168-2.06480.17651330.1487606391
2.0648-2.27260.15371430.14596621100
2.2726-2.60150.16781510.15016596100
2.6015-3.27740.17311490.1533655298
3.2774-46.7150.14391440.137651797

+
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