[English] 日本語
Yorodumi
- PDB-7f8p: Crystal structure of the Mycobacterium tuberculosis L,D-transpept... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f8p
TitleCrystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with new carbapenem drug T203
ComponentsL,D-transpeptidase 2
KeywordsHYDROLASE / L / D-transpeptidase / Cysteine protease
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / 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-56X / Chem-59I / GLUTAMIC ACID / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKumar, P. / Lamichhane, G.
Funding support India, United States, 3items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2019/005079 India
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R33 AI111739 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI137720 United States
CitationJournal: Elife / Year: 2022
Title: Allosteric cooperation in beta-lactam binding to a non-classical transpeptidase.
Authors: Ahmad, N. / Dugad, S. / Chauhan, V. / Ahmed, S. / Sharma, K. / Kachhap, S. / Zaidi, R. / Bishai, W.R. / Lamichhane, G. / Kumar, P.
History
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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: L,D-transpeptidase 2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1768
Polymers79,0642
Non-polymers1,1126
Water15,385854
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5526
Polymers39,5321
Non-polymers1,0205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area16180 Å2
MethodPISA
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6242
Polymers39,5321
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.799, 94.278, 75.707
Angle α, β, γ (deg.)90.000, 93.136, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 39532.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases

-
Non-polymers , 5 types, 860 molecules

#2: Chemical ChemComp-59I / (2R,3R)-3-methyl-4-(2-oxidanylidene-2-propan-2-yloxy-ethyl)sulfanyl-2-[(2R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2,3-dihydro-1H-pyrrole-5-carboxylic acid


Mass: 345.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-56X / (4R,5S,6S)-6-((R)-1-hydroxyethyl)-3-((2-isopropoxy-2-oxoethyl)thio)-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid


Mass: 343.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21NO6S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 57.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% 5000 MME, 200mM Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30.35 Å / Num. obs: 2095305 / % possible obs: 97.4 % / Redundancy: 5 % / Biso Wilson estimate: 11.97 Å2 / CC1/2: 0.97 / CC star: 0.975 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.036 / Rrim(I) all: 0.082 / Rsym value: 0.062 / Net I/σ(I): 23.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4434 / CC1/2: 0.852 / CC star: 0.959 / Rpim(I) all: 0.364 / Rrim(I) all: 0.823 / Rsym value: 0.845 / Χ2: 0.781 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DU7

5du7


Resolution: 1.7→30.35 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1876 3275 2.22 %
Rwork0.1654 144041 -
obs0.1659 147316 80.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 71 854 6199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00645484
X-RAY DIFFRACTIONf_angle_d0.96877514
X-RAY DIFFRACTIONf_chiral_restr0.0598845
X-RAY DIFFRACTIONf_plane_restr0.0051982
X-RAY DIFFRACTIONf_dihedral_angle_d20.6799774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.2585820.24113700X-RAY DIFFRACTION47.38
1.73-1.760.2428920.21643946X-RAY DIFFRACTION50.54
1.76-1.780.2548850.21324054X-RAY DIFFRACTION51.83
1.78-1.820.254820.20534104X-RAY DIFFRACTION52.86
1.82-1.850.23781080.19234309X-RAY DIFFRACTION54.84
1.85-1.880.1856880.18174524X-RAY DIFFRACTION58
1.88-1.920.19281140.17214853X-RAY DIFFRACTION62.18
1.92-1.960.19091130.1685232X-RAY DIFFRACTION66.95
1.96-2.010.19731450.16435672X-RAY DIFFRACTION73.19
2.01-2.060.18051290.16326191X-RAY DIFFRACTION79.76
2.06-2.120.21091500.15686727X-RAY DIFFRACTION85.05
2.12-2.180.20341700.16136983X-RAY DIFFRACTION90.17
2.18-2.250.18091710.16577385X-RAY DIFFRACTION93.97
2.25-2.330.18091770.16727464X-RAY DIFFRACTION96.56
2.33-2.420.22791760.16927647X-RAY DIFFRACTION97.7
2.42-2.530.17561670.17087594X-RAY DIFFRACTION97.78
2.53-2.670.1971770.17447629X-RAY DIFFRACTION98.1
2.67-2.830.18471740.17177650X-RAY DIFFRACTION98.29
2.83-3.050.18371750.1657742X-RAY DIFFRACTION98.42
3.05-3.360.17171850.1567649X-RAY DIFFRACTION98.37
3.36-3.840.1711730.1497639X-RAY DIFFRACTION98.19
3.84-4.840.17031650.14167718X-RAY DIFFRACTION98.91
4.84-30.350.17831770.17937629X-RAY DIFFRACTION97.68

+
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