[English] 日本語
Yorodumi
- PDB-6ewy: RipA Peptidoglycan hydrolase (Rv1477, Mycobacterium tuberculosis)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ewy
TitleRipA Peptidoglycan hydrolase (Rv1477, Mycobacterium tuberculosis) N-terminal domain
ComponentsPeptidoglycan endopeptidase RipA
KeywordsSTRUCTURAL PROTEIN / Periplasmic protein
Function / homology
Function and homology information


cell wall organization or biogenesis / N-acetylmuramoyl-L-alanine amidase activity / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / peptidoglycan-based cell wall / cell wall organization / proteolysis / extracellular region
Similarity search - Function
: / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Peptidoglycan endopeptidase RipA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsSchnell, R. / Steiner, E.M. / Schneider, G. / Guy, J. / Bourenkov, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
RAC-VR Sweden
CitationJournal: Proteins / Year: 2018
Title: The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity.
Authors: Steiner, E.M. / Lyngso, J. / Guy, J.E. / Bourenkov, G. / Lindqvist, Y. / Schneider, T.R. / Pedersen, J.S. / Schneider, G. / Schnell, R.
History
DepositionNov 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidoglycan endopeptidase RipA


Theoretical massNumber of molelcules
Total (without water)23,2751
Polymers23,2751
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, approximately a dimer size derived, SAXS, Monomer at pH 5, dimer at higher pH values, pH 6-8
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.916, 93.960, 138.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

-
Components

#1: Protein Peptidoglycan endopeptidase RipA / Macrophage invasion and intracellular persistence protein A / Resuscitation-promoting factor ...Macrophage invasion and intracellular persistence protein A / Resuscitation-promoting factor interaction partner A / Rpf-interacting protein A


Mass: 23274.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RipA-N-terminal domain
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: ripA, Rv1477 / Plasmid: pNIC28Bsa4
Details (production host): N-terminal His6-tag, removable by TEV cleavage
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53168, Hydrolases; Acting on peptide bonds (peptidases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.15 Å3/Da / Density % sol: 0.61 % / Description: rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.75 / Details: 42% MPD, 0.1M MES pH 5.75

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2015 / Details: mirrors
RadiationMonochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.191→34.987 Å / Num. obs: 12284 / % possible obs: 90.5 % / Observed criterion σ(I): 4 / Redundancy: 5.8 % / Biso Wilson estimate: 67.94 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Net I/σ(I): 14.5
Reflection shellResolution: 2.191→2.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 614 / CC1/2: 0.946 / Rpim(I) all: 0.174 / Rrim(I) all: 0.42 / % possible all: 87.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
autoPROCdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→34.987 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.51
RfactorNum. reflection% reflection
Rfree0.2667 627 5.13 %
Rwork0.2283 --
obs0.2303 12226 79.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 0 98 1596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081508
X-RAY DIFFRACTIONf_angle_d0.9132043
X-RAY DIFFRACTIONf_dihedral_angle_d15.139556
X-RAY DIFFRACTIONf_chiral_restr0.032243
X-RAY DIFFRACTIONf_plane_restr0.004278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.42140.3139890.251641X-RAY DIFFRACTION46
2.4214-2.77170.30891410.25552715X-RAY DIFFRACTION75

+
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