[English] 日本語
Yorodumi
- PDB-8dp4: Beta-lactamase CTX-M-14 T235A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dp4
TitleBeta-lactamase CTX-M-14 T235A
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / antibiotic resistance / CTX-M-14 / Beta-lactam
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: 1.402 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 14, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,9371
Polymers27,9371
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.960, 41.960, 260.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

-
Components

#1: Protein Beta-lactamase


Mass: 27937.490 Da / Num. of mol.: 1 / Mutation: T235A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M SPG buffer pH 6, 25% (w/v) PEG 1500

-
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: Feb 28, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.402→29.67 Å / Num. obs: 46454 / % possible obs: 97.94 % / Redundancy: 11.9 % / Biso Wilson estimate: 13.02 Å2 / Rrim(I) all: 0.113 / Net I/σ(I): 9.4
Reflection shellResolution: 1.402→1.452 Å / Num. unique obs: 4563 / Rrim(I) all: 0.361 / % possible all: 98.87

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
REFMACphasing
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.402→29.67 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 13.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 2295 4.94 %
Rwork0.1617 44159 -
obs0.1627 46454 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.75 Å2 / Biso mean: 17.3264 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: final / Resolution: 1.402→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 0 321 2281
Biso mean---31.46 -
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 (%)
1.402-1.43210.19571410.1701266098
1.4321-1.46540.17631440.1662762100
1.4654-1.5020.181360.15622770100
1.502-1.54260.1861440.15282760100
1.5426-1.5880.16981520.15542737100
1.588-1.63930.20611410.15812784100
1.6393-1.69790.16791680.1562761100
1.6979-1.76590.15461160.15462798100
1.7659-1.84620.17471480.15252778100
1.8462-1.94350.17311360.15162797100
1.9435-2.06530.15831400.1492810100
2.0653-2.22470.18081570.15252832100
2.2247-2.44850.18181570.1543281399
2.4485-2.80250.16971470.1618279097
2.8025-3.530.17991330.1675269392
3.53-29.670.20941350.1798261483
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)
11.3503-0.32490.46071.6953-0.82881.8332-0.08680.03510.2892-0.04550.0551-0.1937-0.14660.07190.10090.1044-0.0220.00070.1302-0.00110.16970.0213.2062-19.0813
20.48720.04740.1581.0017-0.26850.3733-0.0041-0.0240.07180.036-0.00550.0526-0.0358-0.01960.00030.0951-0.0017-0.00180.140.00640.0876-12.55832.7771-12.6628
32.12370.38010.52181.88110.34294.330.0997-0.3098-0.18970.17430.13120.17080.4389-0.3643-0.15440.1502-0.0171-0.00430.20870.02460.2015-28.9075-15.7339-17.1562
42.68570.4120.60631.60960.27342.42860.00730.21680.0229-0.22370.0364-0.02080.0820.0254-0.07380.13450.004-0.00920.1527-0.00180.1317-23.2344-12.5315-26.7487
50.66990.16270.25190.98080.40171.25950.00640.0246-0.07130.01070.04050.0033-0.01540.0192-0.01280.0775-0.0025-0.00060.14160.01220.1002-24.3525-3.3718-16.3167
61.26790.08270.511.0427-0.36420.4214-0.06570.0950.082-0.05960.01220.03480.0059-0.0090.01030.1037-0.00170.00050.15720.01220.1311-22.69028.0362-19.383
70.552-0.74440.03652.3863-0.55160.2027-0.025-0.06150.02740.15740.0313-0.0336-0.0346-0.0103-0.00770.0985-0.0037-0.01060.13660.01470.1164-11.23813.4026-9.7752
80.47220.1310.00060.3939-0.01660.381-0.01790.0712-0.0242-0.03250.0253-0.02450.0353-0.01680.00320.07380.0047-0.00620.12810.00720.0974-7.622-5.1545-17.8376
92.2543-1.21771.39971.3477-1.20611.8436-0.0170.20610.0334-0.014-0.00260.0082-0.10880.09460.00240.0719-0.0092-0.00080.12960.02350.0987-5.64795.5311-22.8638
101.88570.34761.56630.05630.28771.29840.03910.0850.09060.06070.0135-0.0911-0.05110.1782-0.00680.0814-0.00470.00370.14310.01290.11762.37544.9317-22.5933
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 85 )A51 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 101 )A86 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 128 )A102 - 128
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 155 )A129 - 155
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 179 )A156 - 179
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 194 )A180 - 194
8X-RAY DIFFRACTION8chain 'A' and (resid 195 through 251 )A195 - 251
9X-RAY DIFFRACTION9chain 'A' and (resid 252 through 275 )A252 - 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://pdbjlvh1.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