[English] 日本語
Yorodumi
- PDB-5du7: Crystal structure of ldtMt2 at 1.79 Angstrom resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5du7
TitleCrystal structure of ldtMt2 at 1.79 Angstrom resolution
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / Peptidoglycan synthesis enzyme / cell wall enzyme
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
Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / 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. ...Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / 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. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
L,D-transpeptidase 2 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsKumar, P. / Lamichhane, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP2OD008459-01 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Non-classical transpeptidases yield insight into new antibacterials.
Authors: Kumar, P. / Kaushik, A. / Lloyd, E.P. / Li, S.G. / Mattoo, R. / Ammerman, N.C. / Bell, D.T. / Perryman, A.L. / Zandi, T.A. / Ekins, S. / Ginell, S.L. / Townsend, C.A. / Freundlich, J.S. / Lamichhane, G.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L,D-transpeptidase 2
B: L,D-transpeptidase 2
D: L,D-transpeptidase 2
C: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)158,1284
Polymers158,1284
Non-polymers00
Water32,9131827
1
A: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)39,5321
Polymers39,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)39,5321
Polymers39,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)39,5321
Polymers39,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)39,5321
Polymers39,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: L,D-transpeptidase 2

D: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)79,0642
Polymers79,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1770 Å2
ΔGint-16 kcal/mol
Surface area30850 Å2
MethodPISA
6
B: L,D-transpeptidase 2
C: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)79,0642
Polymers79,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-15 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.644, 75.534, 94.143
Angle α, β, γ (deg.)89.040, 89.960, 92.760
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 39532.004 Da / Num. of mol.: 4 / Fragment: residues 42-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: ldtB, MT2594, V735_02606 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53223, UniProt: I6Y9J2*PLUS, Transferases; Acyltransferases; Aminoacyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1827 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG5000MME, 0.2mM Ammonium sulfate / PH range: pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 153919 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.041 / Rrim(I) all: 0.078 / Χ2: 0.768 / Net I/av σ(I): 14.832 / Net I/σ(I): 7.6 / Num. measured all: 676223
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.7-1.733.50.888170.5770.5440.66995.7
1.73-1.763.70.76989470.6690.4660.69195.80.9
1.76-1.793.70.65488740.7110.3930.71396.10.763
1.79-1.833.80.52688940.8040.3150.73896.10.614
1.83-1.873.80.43889790.8480.2620.75596.40.511
1.87-1.913.80.33389440.8890.1990.81796.40.388
1.91-1.963.80.2889730.9020.1680.86196.70.327
1.96-2.023.80.22989540.9140.1370.85696.80.266
2.02-2.073.80.18590320.9270.1110.865970.216
2.07-2.143.80.15689570.940.0930.89897.20.182
2.14-2.223.80.13390760.9410.080.84497.30.155
2.22-2.313.80.11690680.950.0690.86297.50.135
2.31-2.413.80.10390220.9590.0620.86397.70.12
2.41-2.543.80.08991300.9620.0530.854980.104
2.54-2.73.80.07991130.9660.0470.84998.10.092
2.7-2.913.80.06991370.970.0410.80598.40.081
2.91-3.23.80.06191330.9720.0370.77898.60.072
3.2-3.663.70.05491920.9790.0320.695990.063
3.66-4.613.70.04691870.9850.0280.52799.20.054
4.61-503.70.04291280.9890.0250.38798.30.049

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYN

3vyn


Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2147 / WRfactor Rwork: 0.1714 / FOM work R set: 0.8531 / SU B: 2.685 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1141 / SU Rfree: 0.1143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 7371 4.9 %RANDOM
Rwork0.1696 ---
obs0.1716 144115 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.66 Å2 / Biso mean: 17.48 Å2 / Biso min: 3.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.04 Å20.1 Å2
2---0.25 Å2-0.07 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10558 0 0 1827 12385
Biso mean---30.73 -
Num. residues----1399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910870
X-RAY DIFFRACTIONr_bond_other_d0.0020.029993
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.92614877
X-RAY DIFFRACTIONr_angle_other_deg1.103322919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36451399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34924.093474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.948151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4121566
X-RAY DIFFRACTIONr_chiral_restr0.1540.21669
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022519
X-RAY DIFFRACTIONr_mcbond_it1.5661.4585611
X-RAY DIFFRACTIONr_mcbond_other1.5661.4585610
X-RAY DIFFRACTIONr_mcangle_it2.3982.1767005
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 414 -
Rwork0.243 7673 -
all-8087 -
obs--68.39 %

+
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