[English] 日本語
Yorodumi
- PDB-6ooj: CTX-M-14 Beta Lactamase with Compound 14 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ooj
TitleCTX-M-14 Beta Lactamase with Compound 14
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / Beta-Lactamase / ESBL / Non covalent complex / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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-J1X / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKemp, M. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
CitationJournal: Org Chem Front / Year: 2019
Title: An Empirical Study of Amide-Heteroarene pi-Stacking Interactions Using Reversible Inhibitors of a Bacterial Serine Hydrolase.
Authors: DeFrees, K. / Kemp, M.T. / ElHilali-Pollard, X. / Zhang, X. / Mohamed, A. / Chen, Y. / Renslo, A.R.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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)57,5646
Polymers55,9672
Non-polymers1,5974
Water13,151730
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7823
Polymers27,9841
Non-polymers7992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7823
Polymers27,9841
Non-polymers7992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.096, 106.929, 47.830
Angle α, β, γ (deg.)90.000, 101.610, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-lactamase


Mass: 27983.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-14 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2S1PK93, UniProt: Q9L5C7*PLUS, beta-lactamase
#2: Chemical
ChemComp-J1X / 3-(1H-pyrazol-1-yl)-N-[3-(1H-tetrazol-5-yl)phenyl]-5-(trifluoromethyl)benzamide


Mass: 399.329 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C18H12F3N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 1.0 M potassium phosphate, pH 7.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 86936 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.059 / Χ2: 0.848 / Net I/σ(I): 11.7 / Num. measured all: 319818
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.422.90.31942700.8680.2140.3860.79999.6
1.42-1.453.20.29343980.9060.1890.350.83499.8
1.45-1.483.40.2742750.9230.1660.3180.84999.8
1.48-1.513.70.24643820.9510.1460.2860.884100
1.51-1.543.70.21843360.9560.1290.2540.905100
1.54-1.583.70.19242940.9650.1140.2230.906100
1.58-1.623.70.16943400.9720.10.1960.902100
1.62-1.663.70.15243560.9770.090.1770.894100
1.66-1.713.80.13243520.9820.0780.1540.884100
1.71-1.763.80.11343350.9850.0670.1320.88100
1.76-1.833.80.09643280.9890.0570.1120.876100
1.83-1.93.80.0843800.9930.0470.0930.874100
1.9-1.993.80.06543280.9940.0380.0750.959100
1.99-2.093.80.0543430.9960.030.0580.867100
2.09-2.223.80.04443480.9960.0260.0510.849100
2.22-2.393.80.0443770.9970.0240.0470.896100
2.39-2.633.80.03243540.9980.0190.0380.771100
2.63-3.023.80.02743550.9980.0160.0320.711100
3.02-3.83.80.02243760.9990.0130.0250.728100
3.8-503.70.02144090.9980.0130.0240.67599.5

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UA6

4ua6


Resolution: 1.4→25.714 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.07
RfactorNum. reflection% reflection
Rfree0.1649 2988 2.34 %
Rwork0.1388 --
obs0.1395 127812 74.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.36 Å2 / Biso mean: 17.8132 Å2 / Biso min: 7.73 Å2
Refinement stepCycle: final / Resolution: 1.4→25.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 145 730 4782
Biso mean--15.15 29.67 -
Num. residues----523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4002-1.42310.2302820.193496357844
1.4231-1.44770.2106850.17773761384646
1.4477-1.4740.1836920.17363841393348
1.474-1.50230.20051010.17174076417751
1.5023-1.5330.1797990.16224151425052
1.533-1.56630.22171110.15634380449155
1.5663-1.60280.1876950.14794674476958
1.6028-1.64280.18211160.13995016513263
1.6428-1.68730.15521430.14785269541266
1.6873-1.73690.14671460.15365758590471
1.7369-1.79290.21541460.15376115626176
1.7929-1.8570.16221540.1496446660081
1.857-1.93130.17691700.14276750692084
1.9313-2.01920.19061480.14017031717987
2.0192-2.12560.17761750.13667250742591
2.1256-2.25870.13851790.13237551773093
2.2587-2.4330.20131860.13737577776395
2.433-2.67760.1481790.14037833801298
2.6776-3.06450.16971980.14347928812699
3.0645-3.85890.15281780.128679698147100
3.8589-25.71820.14422050.12747952815799

+
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