[English] 日本語
Yorodumi
- PDB-5dc2: X-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dc2
TitleX-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDUCT OF L,D-TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / L / D-Transpeptidase / CARBAPENEMS BIAPENEM-ADDUCT / LDTMT2 / MYCOBACTERIUM TUBERCULOSIS
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 ...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
(4S)-4-methyl-2,5,7-trioxoheptanoic acid / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L,D-transpeptidase 2 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.182 Å
AuthorsPan, Y. / Basta, L. / Lamichhane, G. / Bianchet, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI111739 United States
Citation
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.
#1: 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
DepositionAug 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.name
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
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)79,21135
Polymers75,5882
Non-polymers3,62433
Water10,845602
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,52417
Polymers37,7941
Non-polymers1,73016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,68818
Polymers37,7941
Non-polymers1,89417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.822, 93.354, 75.243
Angle α, β, γ (deg.)90.00, 92.61, 90.00
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: 37793.934 Da / Num. of mol.: 2 / Fragment: UNP residues 56-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: ldtB, MT2594, V735_02606 / Production host: Escherichia coli (E. coli)
References: UniProt: O53223, UniProt: I6Y9J2*PLUS, Transferases; Acyltransferases; Aminoacyltransferases

-
Non-polymers , 7 types, 635 molecules

#2: Chemical ChemComp-58U / (4S)-4-methyl-2,5,7-trioxoheptanoic acid


Mass: 186.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10O5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.82 Å3/Da / Density % sol: 56.46 % / Description: Thin Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18 % v/v PEG MME 500 0.2 M Amonium Sulfate Tris HCl 100mM NaCl
PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5146 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5146 Å / Relative weight: 1
ReflectionResolution: 2.05→37.015 Å / Num. obs: 47794 / % possible obs: 90.9 % / Redundancy: 3.5 % / Rsym value: 0.063 / Net I/σ(I): 193.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.36 / % possible all: 50.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.182→37.015 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 4162 5.01 %random selection
Rwork0.1595 ---
obs0.162 83073 96.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.182→37.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 201 602 6125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095729
X-RAY DIFFRACTIONf_angle_d1.0697802
X-RAY DIFFRACTIONf_dihedral_angle_d13.0472022
X-RAY DIFFRACTIONf_chiral_restr0.057853
X-RAY DIFFRACTIONf_plane_restr0.0051015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1821-2.20690.26321030.18092037X-RAY DIFFRACTION76
2.2069-2.23290.23221440.17772467X-RAY DIFFRACTION91
2.2329-2.26010.25091120.17552623X-RAY DIFFRACTION96
2.2601-2.28870.24061340.16922632X-RAY DIFFRACTION96
2.2887-2.31880.26711190.16882631X-RAY DIFFRACTION97
2.3188-2.35060.24841360.19242685X-RAY DIFFRACTION96
2.3506-2.38410.27481430.18972535X-RAY DIFFRACTION97
2.3841-2.41970.30061570.17862709X-RAY DIFFRACTION96
2.4197-2.45750.2541550.18882631X-RAY DIFFRACTION98
2.4575-2.49780.26691060.17662607X-RAY DIFFRACTION96
2.4978-2.54090.24561600.18292697X-RAY DIFFRACTION98
2.5409-2.58710.27511570.1932566X-RAY DIFFRACTION97
2.5871-2.63680.31441280.18312673X-RAY DIFFRACTION98
2.6368-2.69060.26321770.18962587X-RAY DIFFRACTION96
2.6906-2.74910.27021190.19782712X-RAY DIFFRACTION98
2.7491-2.8130.30721170.2042626X-RAY DIFFRACTION96
2.813-2.88330.29781370.20512642X-RAY DIFFRACTION96
2.8833-2.96130.29611220.18842642X-RAY DIFFRACTION97
2.9613-3.04840.24741380.19082647X-RAY DIFFRACTION97
3.0484-3.14670.22391240.17642684X-RAY DIFFRACTION98
3.1467-3.25910.21121440.17172699X-RAY DIFFRACTION99
3.2591-3.38950.20441360.15582702X-RAY DIFFRACTION99
3.3895-3.54370.17511570.13882643X-RAY DIFFRACTION99
3.5437-3.73030.19951410.13592703X-RAY DIFFRACTION99
3.7303-3.96380.16581300.12782719X-RAY DIFFRACTION99
3.9638-4.26940.13041320.12122714X-RAY DIFFRACTION99
4.2694-4.69830.14031700.11062680X-RAY DIFFRACTION99
4.6983-5.37640.15271480.12952644X-RAY DIFFRACTION99
5.3764-6.7670.16911660.16372691X-RAY DIFFRACTION99
6.767-37.02040.20161500.17292683X-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)
12.8102-2.19420.44786.25722.04553.3433-0.0148-0.13120.16250.1380.0755-0.1353-0.02180.1198-0.03990.1749-0.03120.02020.17610.02260.19696.0652.8458110.701
21.7279-2.2825-0.48916.9902-2.21163.7005-0.0823-0.048-0.09330.05060.05040.0540.1455-0.19270.0470.1786-0.05090.00610.2652-0.02110.2022-14.86-28.973974.4631
31.4644-0.94012.30821.3693-1.21477.7046-0.0204-0.11650.02550.00480.07420.0203-0.1033-0.1328-0.04830.1566-0.04040.05520.2249-0.00520.22727.6863-9.763180.6064
41.5720.02520.15792.2831-0.81111.98470.19920.0588-0.1857-0.1143-0.224-0.10320.11850.07140.03190.21470.0005-0.02330.2121-0.00520.211414.0442-15.775956.9871
52.1493-0.5796-2.17580.99431.08615.61350.0332-0.0656-0.12110.023-0.00070.06390.0025-0.1882-0.01870.1826-0.0251-0.02560.15290.01390.2036-12.7768-16.655144.2525
62.20240.0780.71131.62640.55481.6520.12810.27180.1029-0.1636-0.2030.1342-0.1643-0.09570.06770.24620.03990.00960.22820.00810.2119-17.3032-10.63320.5977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resseq 56:147
2X-RAY DIFFRACTION2chain 'B' and resseq 56:147
3X-RAY DIFFRACTION3chain 'A' and resseq 148:251
4X-RAY DIFFRACTION4chain 'A' and resseq 252:407
5X-RAY DIFFRACTION5chain 'B' and resseq 148:251
6X-RAY DIFFRACTION6chain 'B' and resseq 252:407

+
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://pdbjlc1.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