[English] 日本語
Yorodumi
- PDB-8a1k: Crystal structure of the transpeptidase LdtMt2 from Mycobacterium... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a1k
TitleCrystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with ebsulfur analogue 15
ComponentsL,D-transpeptidase 2
KeywordsANTIMICROBIAL PROTEIN / L / D-transpeptidase / LdtMt2 / Inhibitor / Covalent
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region ...peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-KT6 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
Authorsde Munnik, M. / Lang, P.A. / Brem, J. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: High-throughput screen with the l,d-transpeptidase Ldt Mt2 of Mycobacterium tuberculosis reveals novel classes of covalently reacting inhibitors.
Authors: de Munnik, M. / Lang, P.A. / De Dios Anton, F. / Cacho, M. / Bates, R.H. / Brem, J. / Rodriguez Miquel, B. / Schofield, C.J.
History
DepositionJun 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: 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 1.2Feb 7, 2024Group: 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: L,D-transpeptidase 2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7768
Polymers76,0182
Non-polymers7586
Water17,853991
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3373
Polymers38,0091
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4385
Polymers38,0091
Non-polymers4294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.977, 95.169, 75.624
Angle α, β, γ (deg.)90.000, 92.350, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein L,D-transpeptidase 2 / LDT 2 / Ldt(Mt2)


Mass: 38009.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ldtB, MT2594, V735_02606 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53223, Transferases; Acyltransferases; Aminoacyltransferases

-
Non-polymers , 5 types, 997 molecules

#2: Chemical ChemComp-KT6 / 4,5-bis(chloranyl)-N-(2-hydroxyethyl)-2-sulfanyl-benzamide / 5,6-Dichloro-2-(2-hydroxyethyl)-1,2-benzisothiazol-3-one (reacted form of)


Mass: 266.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9Cl2NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium nitrate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→60.9 Å / Num. obs: 86825 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.786.60.773143230.7940.3260.84100
4.75-60.947.10.02877.744300.9910.0120.0399.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.18 Å60.98 Å

-
Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
XDSdata reduction
xia2data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RRM

6rrm


Resolution: 1.75→48.409 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 4357 5.03 %
Rwork0.1747 82241 -
obs0.1763 86598 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.6 Å2 / Biso mean: 34.6294 Å2 / Biso min: 14.19 Å2
Refinement stepCycle: final / Resolution: 1.75→48.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 43 991 6246
Biso mean--40.01 43.27 -
Num. residues----700
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7502-1.77010.31521360.2911271798
1.7701-1.79090.25841310.2555275799
1.7909-1.81270.30871280.25012685100
1.8127-1.83570.27361620.24312754100
1.8357-1.85980.26431400.23482712100
1.8598-1.88530.23951430.22832735100
1.8853-1.91220.33231470.2695273699
1.9122-1.94080.39421360.3587272799
1.9408-1.97110.29831360.22332717100
1.9711-2.00340.22931410.20562728100
2.0034-2.0380.21541430.19762734100
2.038-2.0750.22781380.1948273999
2.075-2.11490.22081530.18132751100
2.1149-2.15810.23881490.18372709100
2.1581-2.2050.23081360.19732768100
2.205-2.25630.31141470.26292738100
2.2563-2.31280.2641340.20842716100
2.3128-2.37530.20711580.1792741100
2.3753-2.44520.23171440.17332770100
2.4452-2.52410.19951520.16732720100
2.5241-2.61430.21421220.16322764100
2.6143-2.7190.21011420.17212751100
2.719-2.84270.23371450.16812723100
2.8427-2.99260.2081430.16172788100
2.9926-3.180.19431610.16452738100
3.18-3.42550.20511480.1542767100
3.4255-3.77010.17541550.15022746100
3.7701-4.31530.15461460.13162768100
4.3153-5.43570.13991650.12412756100
5.4357-48.4090.17531760.184278699
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)
16.29191.26970.29745.05010.90754.48580.0613-0.1486-0.2102-0.46650.10980.4441-0.1765-0.6966-0.17820.32080.015-0.02820.39960.05370.32228.0826-9.72520.9506
21.02772.4818-1.20699.17261.70958.1422-0.1605-0.2557-0.17370.01140.2050.04190.0929-0.0628-0.03360.20420.06370.00510.3548-0.00020.246711.9065-19.62761.1535
30.87050.2819-0.08881.85362.13867.62390.05810.2324-0.1073-0.30410.5037-0.0228-0.20560.3453-0.47490.21690.0253-0.00160.36030.02120.278315.1593-10.02896.2796
41.11210.15620.68010.87840.69593.21130.0865-0.0248-0.0113-0.0731-0.0063-0.027-0.04660.0239-0.07330.1350.02550.030.12030.00960.21217.8689-1.457839.6619
53.42020.77872.31110.44420.64242.35710.1282-0.1591-0.1509-0.0166-0.0352-0.15980.05030.2064-0.09770.18460.00290.02980.23410.00140.242120.70751.657650.3472
62.91270.02541.34150.78440.17082.29920.0588-0.26150.13950.051-0.064-0.0596-0.05860.0621-0.00260.1578-0.00920.03710.163-0.01450.20214.88114.714153.2804
73.49012.5020.2585.6657-1.60271.75540.1492-0.02120.34790.0018-0.1365-0.0327-0.09950.0101-0.01480.15720.02990.04330.1552-0.00540.2299-10.470517.5497-33.4169
81.17880.3561-0.4622.9217-2.19115.4638-0.0346-0.01470.0662-0.2870.1978-0.02950.1706-0.0478-0.14320.11390.02980.01130.1366-0.02670.2315-14.242911.4187-32.156
90.09970.50490.5559-0.1192-0.00183.18150.11330.1146-0.06370.08390.123-0.0680.07720.4026-0.18640.33130.1732-0.0230.3712-0.04810.287-10.70623.55173.8286
109.4331-0.2521-1.14650.05230.36452.69740.43590.6652-0.31230.0812-0.1981-0.00220.2793-0.4267-0.22210.44040.1151-0.10060.3766-0.03390.2295-24.3830.154613.439
114.20430.88890.31066.57014.09984.37130.4906-0.0208-1.24470.0673-0.24260.59480.6252-0.219-0.16310.47090.0358-0.22290.4109-0.05130.7342-32.7506-8.460317.2861
122.95680.8648-1.07441.88461.03883.65520.27390.0502-0.1541-0.109-0.18940.21480.1964-0.1601-0.07860.31320.0887-0.10460.2468-0.01720.2607-20.41381.321321.8823
130.9698-0.45470.1350.73820.03770.04510.36350.4801-0.4684-0.069-0.0822-0.28550.44530.33390.20790.53640.7569-0.210.3918-0.18930.3802-7.3084-6.98376.1531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 79 )A58 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 110 )A80 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 157 )A111 - 157
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 289 )A158 - 289
5X-RAY DIFFRACTION5chain 'A' and (resid 290 through 308 )A290 - 308
6X-RAY DIFFRACTION6chain 'A' and (resid 309 through 407 )A309 - 407
7X-RAY DIFFRACTION7chain 'B' and (resid 58 through 122 )B58 - 122
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 157 )B123 - 157
9X-RAY DIFFRACTION9chain 'B' and (resid 158 through 289 )B158 - 289
10X-RAY DIFFRACTION10chain 'B' and (resid 290 through 308 )B290 - 308
11X-RAY DIFFRACTION11chain 'B' and (resid 309 through 323 )B309 - 323
12X-RAY DIFFRACTION12chain 'B' and (resid 324 through 378 )B324 - 378
13X-RAY DIFFRACTION13chain 'B' and (resid 379 through 407 )B379 - 407

+
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