[English] 日本語
Yorodumi
- PDB-4qr7: Structure and specificity of L-D-Transpeptidase from Mycobacteriu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qr7
TitleStructure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
ComponentsL,d-transpeptidase LdtB
KeywordsHYDROLASE / Structural Genomics / Enzyme Function Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / L-D-transpeptidase / D-D-transpeptidase / Single anomalous diffraction / imipenem / meropenem / peptidoglycan / beta-lactamase
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
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-like / L,D-transpeptidase catalytic domain ...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-like / L,D-transpeptidase catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-DWZ / Chem-MLD / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.303 Å
AuthorsGokulan, K. / Varughese, K.I.
CitationJournal: To be Published
Title: Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
Authors: Gokulan, K. / Khare, S. / Cerniglia, C.E. / Foley, S.L. / Varughese, K.I.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 2, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L,d-transpeptidase LdtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9863
Polymers37,6791
Non-polymers1,3072
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: L,d-transpeptidase LdtB
hetero molecules

A: L,d-transpeptidase LdtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9726
Polymers75,3582
Non-polymers2,6154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area3200 Å2
ΔGint-17 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.330, 66.459, 206.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

-
Components

#1: Protein L,d-transpeptidase LdtB / Probable L / D-transpeptidase LdtB


Mass: 37678.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: ldtB, Rv2518c, RVBD_2518c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: I6Y9J2
#2: Chemical ChemComp-MLD / GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA / 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2-ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELYL-D-ALANINE


Mass: 921.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H59N7O20
#3: Chemical ChemComp-DWZ / (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium malonate (pH 7.0) and 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→103.4 Å / Rmerge(I) obs: 0.0556 / Net I/σ(I): 13.98

-
Processing

Software
NameVersionClassification
HKL-2000data collection
Auto-Rickshawphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.303→33.249 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 814 5 %
Rwork0.2028 --
obs0.2059 16293 90.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→33.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2634 0 80 80 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082700
X-RAY DIFFRACTIONf_angle_d1.1793697
X-RAY DIFFRACTIONf_dihedral_angle_d12.874941
X-RAY DIFFRACTIONf_chiral_restr0.077414
X-RAY DIFFRACTIONf_plane_restr0.005486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3027-2.44690.33681390.24162309X-RAY DIFFRACTION84
2.4469-2.63580.30541260.24382489X-RAY DIFFRACTION89
2.6358-2.90090.30971410.23872549X-RAY DIFFRACTION91
2.9009-3.32030.28881110.23022631X-RAY DIFFRACTION92
3.3203-4.18190.26221600.18812697X-RAY DIFFRACTION95
4.1819-33.25280.21131370.16722804X-RAY DIFFRACTION94

+
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