[English] 日本語
Yorodumi
- PDB-6boi: Crystal Structure of LdtMt2 (56-408) with a panipenem adduct at t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6boi
TitleCrystal Structure of LdtMt2 (56-408) with a panipenem adduct at the active site cysteine-354
ComponentsPutative conserved lipoprotein LppS
KeywordsTRANSFERASE / L / D-Transpeptidase 2 / Carbapenem / Complex
Function / homology
Function and homology information


acyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / membrane
Similarity search - Function
Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain ...Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-E0Y / DI(HYDROXYETHYL)ETHER / Conserved lipoprotein LppS
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsSaavedra, H. / Bianchet, M.A.
Citation
Journal: To Be Published
Title: Structures and Mechanism of Inhibition of Mycobacterium tuberculosis L,D-transpeptidase 2 by Panipenem
Authors: Saavedra, H. / Bianchet, M.A.
#1: Journal: BMC Biochem. / Year: 2017
Title: Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem.
Authors: Bianchet, M.A. / Pan, Y.H. / Basta, L.A.B. / Saavedra, H. / Lloyd, E.P. / Kumar, P. / Mattoo, R. / Townsend, C.A. / Lamichhane, G.
#2: Journal: J. Biol. Chem. / Year: 2015
Title: Loss of a Functionally and Structurally Distinct ld-Transpeptidase, LdtMt5, Compromises Cell Wall Integrity in Mycobacterium tuberculosis.
Authors: Brammer Basta, L.A. / Ghosh, A. / Pan, Y. / Jakoncic, J. / Lloyd, E.P. / Townsend, C.A. / Lamichhane, G. / Bianchet, M.A.
#3: Journal: Structure / Year: 2012
Title: Targeting the cell wall of Mycobacterium tuberculosis: structure and mechanism of L,D-transpeptidase 2.
Authors: Erdemli, S.B. / Gupta, R. / Bishai, W.R. / Lamichhane, G. / Amzel, L.M. / Bianchet, M.A.
History
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative conserved lipoprotein LppS
B: Putative conserved lipoprotein LppS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,58019
Polymers75,4462
Non-polymers2,13417
Water8,791488
1
A: Putative conserved lipoprotein LppS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,01912
Polymers37,7231
Non-polymers1,29611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative conserved lipoprotein LppS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5617
Polymers37,7231
Non-polymers8386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.060, 94.060, 75.400
Angle α, β, γ (deg.)90.00, 92.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative conserved lipoprotein LppS


Mass: 37722.855 Da / Num. of mol.: 2 / Fragment: residues 56-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: lppS, MRA_2545 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U5L6

-
Non-polymers , 5 types, 505 molecules

#2: Chemical ChemComp-E0Y / (3S,5R)-5-[(2R,3R)-1,3-dihydroxybutan-2-yl]-3-({(3R)-1-[(1E)-ethanimidoyl]pyrrolidin-3-yl}sulfanyl)-L-proline


Type: L-peptide linking / Mass: 345.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H27N3O4S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 17% v/v PEG mono-methyl ester 5000 and 180 mM ammonium sulfate, Crystals were soaked in 4 mM of panipenem for 15 minutes

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.102→51.175 Å / Num. obs: 45570 / % possible obs: 91.94 % / Redundancy: 3.6 % / Net I/σ(I): 30

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D7H

5d7h


Resolution: 2.102→51.175 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.48
RfactorNum. reflection% reflection
Rfree0.2006 2297 5.04 %
Rwork0.1618 --
obs0.1638 45570 91.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→51.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 134 488 5938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115599
X-RAY DIFFRACTIONf_angle_d1.1347653
X-RAY DIFFRACTIONf_dihedral_angle_d14.643217
X-RAY DIFFRACTIONf_chiral_restr0.064845
X-RAY DIFFRACTIONf_plane_restr0.006997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1019-2.14760.2618860.19521615X-RAY DIFFRACTION55
2.1476-2.19760.24581060.20111857X-RAY DIFFRACTION64
2.1976-2.25260.24171140.19692091X-RAY DIFFRACTION72
2.2526-2.31350.24541150.1942511X-RAY DIFFRACTION85
2.3135-2.38150.26391450.18722897X-RAY DIFFRACTION99
2.3815-2.45840.22811640.19192895X-RAY DIFFRACTION99
2.4584-2.54630.24051530.18632931X-RAY DIFFRACTION99
2.5463-2.64820.26741630.18672911X-RAY DIFFRACTION100
2.6482-2.76870.2351640.17812914X-RAY DIFFRACTION99
2.7687-2.91470.21991410.17612957X-RAY DIFFRACTION100
2.9147-3.09730.20151470.16342936X-RAY DIFFRACTION100
3.0973-3.33640.20161500.16022933X-RAY DIFFRACTION100
3.3364-3.67210.18831630.15092939X-RAY DIFFRACTION100
3.6721-4.20320.16941340.14242963X-RAY DIFFRACTION100
4.2032-5.29470.16681830.13082935X-RAY DIFFRACTION100
5.2947-51.19010.18921690.16592988X-RAY DIFFRACTION99
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)
12.22453.11160.2317.59613.0464.486-0.16720.097-0.088-0.01730.1851-0.02310.05080.14590.01510.24440.05050.01790.34990.03540.24411.462927.44220.337
21.95070.7079-1.34811.49-0.53954.8472-0.00160.0556-0.0537-0.1019-0.0096-0.0252-0.03310.20190.01570.20950.0313-0.02720.1583-0.00820.20629.158439.864530.9599
32.05710.19160.26792.0647-0.42841.6590.1453-0.34050.15150.2568-0.2784-0.1804-0.24110.12550.1310.3103-0.06140.00150.2648-0.01570.25613.916246.104754.4027
42.7156-2.6371-0.09746.39912.81393.3803-0.02130.04280.05970.1697-0.0067-0.17070.0490.08140.03770.2283-0.04020.02980.20820.0220.23969.560212.536735.6958
51.2567-0.73051.41161.5396-0.78425.1274-0.0596-0.0315-0.0654-0.00660.19330.0607-0.0868-0.0657-0.12480.2255-0.05430.03870.2843-0.0070.284610.98740.20224.9382
61.8485-0.2380.46493.2952-1.14941.25830.33280.119-0.1615-0.4247-0.3265-0.13340.20980.14770.00710.3694-0.0067-0.04040.3611-0.0150.303617.7827-6.1324-18.17
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and ((resseq 56:147))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 148:252))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 253:407))
4X-RAY DIFFRACTION4chain 'A' and ((resseq 56:147))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 148:252))
6X-RAY DIFFRACTION6chain 'A' and ((resseq 253:407))

+
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://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