[English] 日本語
Yorodumi
- PDB-8sj3: Beta-lactamase CTX-M-14 E166Y/N170G -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sj3
TitleBeta-lactamase CTX-M-14 E166Y/N170G
ComponentsBeta-lactamase CTX-M-14
KeywordsHYDROLASE / beta-lactamase / enzyme / serine protease / antimicrobial resistance
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/transpeptidase-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJudge, A. / Palzkill, T. / Sankaran, B. / Prasad, B.V.V. / Hu, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)32956 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning.
Authors: Judge, A. / Sankaran, B. / Hu, L. / Palaniappan, M. / Birgy, A. / Prasad, B.V.V. / Palzkill, T.
History
DepositionApr 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase CTX-M-14
B: Beta-lactamase CTX-M-14


Theoretical massNumber of molelcules
Total (without water)55,9552
Polymers55,9552
Non-polymers00
Water9,116506
1
A: Beta-lactamase CTX-M-14


Theoretical massNumber of molelcules
Total (without water)27,9781
Polymers27,9781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase CTX-M-14


Theoretical massNumber of molelcules
Total (without water)27,9781
Polymers27,9781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.371, 42.371, 262.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

-
Components

#1: Protein Beta-lactamase CTX-M-14


Mass: 27977.557 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M ammonium chloride, 0.1 M sodium acetate, 20% w/v PEG 6,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999889 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2021
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999889 Å / Relative weight: 1
ReflectionResolution: 1.5→32.97 Å / Num. obs: 70681 / % possible obs: 96 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.5 Å2 / CC1/2: 0.82 / Net I/σ(I): 3.26
Reflection shellResolution: 1.5→1.554 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 7283 / CC1/2: 0.487

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMv7.2.2data reduction
SCALAv3.3.8data scaling
PHASERv2.1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→32.97 Å / SU ML: 0.1685 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.1136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1976 3416 4.91 %
Rwork0.1424 66117 -
obs0.1452 69533 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 0 506 4397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00584152
X-RAY DIFFRACTIONf_angle_d0.90675675
X-RAY DIFFRACTIONf_chiral_restr0.0743668
X-RAY DIFFRACTIONf_plane_restr0.0084747
X-RAY DIFFRACTIONf_dihedral_angle_d5.8334611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.26211270.17062399X-RAY DIFFRACTION83.26
1.52-1.540.24181250.15992596X-RAY DIFFRACTION88.89
1.54-1.570.25631470.14312782X-RAY DIFFRACTION94.3
1.57-1.590.2561610.14472753X-RAY DIFFRACTION97.17
1.59-1.620.21191390.1372914X-RAY DIFFRACTION98.8
1.62-1.650.21731550.13612852X-RAY DIFFRACTION99.47
1.65-1.680.23081540.1422890X-RAY DIFFRACTION99.09
1.68-1.720.22491490.14332861X-RAY DIFFRACTION98.59
1.72-1.750.29281180.14592951X-RAY DIFFRACTION98.9
1.75-1.790.22611350.14362809X-RAY DIFFRACTION98.59
1.79-1.840.25871590.13572888X-RAY DIFFRACTION97.82
1.84-1.890.20591540.12962760X-RAY DIFFRACTION97
1.89-1.950.21161620.12562810X-RAY DIFFRACTION96.68
1.95-2.010.2121330.12842831X-RAY DIFFRACTION96.05
2.01-2.080.19431340.13272752X-RAY DIFFRACTION95.5
2.08-2.160.1821140.13582788X-RAY DIFFRACTION94.84
2.16-2.260.20421330.13652736X-RAY DIFFRACTION94.13
2.26-2.380.21261080.1462729X-RAY DIFFRACTION92.17
2.38-2.530.19441710.14572668X-RAY DIFFRACTION93.02
2.53-2.720.20991500.14962642X-RAY DIFFRACTION90.97
2.72-30.16321500.15662643X-RAY DIFFRACTION90.36
3-3.430.17321250.14922602X-RAY DIFFRACTION90.03
3.43-4.320.18071440.13682616X-RAY DIFFRACTION89.61
4.32-32.970.16261690.14662845X-RAY DIFFRACTION97.83

+
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