[English] 日本語
Yorodumi
- PDB-8dod: Beta-lactamase CTX-M-14 S130A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dod
TitleBeta-lactamase CTX-M-14 S130A
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / CTX-M-14 / mutation / B-lactam / antibiotic 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: 1.61 Å
AuthorsLu, S. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Mutagenesis and structural analysis reveal the CTX-M beta-lactamase active site is optimized for cephalosporin catalysis and drug resistance.
Authors: Lu, S. / Montoya, M. / Hu, L. / Neetu, N. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionJul 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0072
Polymers27,9681
Non-polymers391
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.490, 41.490, 230.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Beta-lactamase


Mass: 27967.516 Da / Num. of mol.: 1 / Mutation: S130A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: H6UQI0, beta-lactamase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl pH 8.5, 25% (W/V) PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.61→35.504 Å / Num. obs: 62179 / % possible obs: 99.46 % / Redundancy: 2 % / Biso Wilson estimate: 17.44 Å2 / Rmerge(I) obs: 0.0143 / Rrim(I) all: 0.02023 / Net I/σ(I): 20.94
Reflection shellResolution: 1.61→1.668 Å / Rmerge(I) obs: 0.0634 / Num. unique obs: 6092 / Rrim(I) all: 0.09381 / % possible all: 99.25

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.61→35.504 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2004 6.45 %
Rwork0.2218 29080 -
obs0.2242 31084 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.76 Å2 / Biso mean: 33.0089 Å2 / Biso min: 10.34 Å2
Refinement stepCycle: final / Resolution: 1.61→35.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 0 207 2170
Biso mean---33.78 -
Num. residues----263
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6101-1.65030.391400.3017202999
1.6503-1.69490.32681380.2811198799
1.6949-1.74480.37051400.2798206799
1.7448-1.80110.32471440.2605206799
1.8011-1.86550.29721390.2651199199
1.8655-1.94020.28131440.25532061100
1.9402-2.02850.31061440.25522029100
2.0285-2.13540.28851350.24742079100
2.1354-2.26920.25981410.23572069100
2.2692-2.44440.27241450.2322109100
2.4444-2.69030.25881380.21852070100
2.6903-3.07940.23181480.21022118100
3.0794-3.87890.22541480.1932214399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84350.1437-0.2160.1562-0.20121.54890.10440.0985-0.2042-0.10130.04220.00330.7877-0.0125-0.12420.7160.1467-0.15220.2757-0.01960.17393.5389-16.3927-31.2385
21.6763-0.4879-0.63731.4688-0.4192.51710.1697-0.0186-0.2892-0.1195-0.0740.09990.8069-0.47650.02760.2586-0.0796-0.09650.24690.02750.1911-5.1541-9.9726-16.3963
33.24141.3919-0.96121.8138-0.52290.89620.1062-0.27680.19060.2103-0.05060.291-0.1434-0.4072-0.08450.22340.05320.07860.54920.02540.2792-12.151311.0298-4.9073
40.7097-0.1127-0.090.57260.03370.34140.0189-0.06850.2366-0.00950.0164-0.0496-0.2826-0.2457-0.0350.24590.16870.04810.28530.06340.2277-7.02712.5342-14.6342
50.7538-0.2195-0.02281.08020.33011.89150.13490.06770.0833-0.00990.106-0.12440.2945-0.0632-0.17120.1094-0.003-0.02660.14610.02070.15110.8541-2.399-9.2969
62.0389-0.18040.02610.66950.07490.1733-0.04830.0544-0.21230.01250.0320.09920.3174-0.212-0.00450.4736-0.1961-0.05230.25320.03210.1811-6.0975-13.0818-16.7228
70.3702-0.2030.08220.1158-0.02870.07740.0326-0.0302-0.1080.0338-0.00810.1080.1098-0.2644-0.06360.2086-0.2666-0.07150.79510.06980.2238-18.0783-4.6798-15.6966
80.6236-0.4411-0.43091.1929-0.28760.6949-0.04690.15310.0044-0.10820.13570.20320.0535-0.5264-0.01760.1362-0.0231-0.02860.33330.04540.1584-9.139-2.8149-31.954
91.18730.0830.50020.5861-0.18090.95640.05530.2049-0.1105-0.07920.13540.03020.4186-0.0884-0.12130.1307-0.0457-0.0330.349-0.01030.1785-1.0765-5.5373-26.189
102.61610.20350.07882.61210.48042.52770.14580.2408-0.2328-0.19950.10020.12660.6424-0.3994-0.14250.3743-0.055-0.07120.22350.01050.1638-2.4548-10.4338-34.7005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 50 )A26 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 86 )A51 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 101 )A87 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 129 )A102 - 129
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 179 )A130 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 194 )A180 - 194
7X-RAY DIFFRACTION7chain 'A' and (resid 195 through 212 )A195 - 212
8X-RAY DIFFRACTION8chain 'A' and (resid 213 through 229 )A213 - 229
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 275 )A230 - 275
10X-RAY DIFFRACTION10chain 'A' and (resid 276 through 290 )A276 - 290

+
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