[English] 日本語
Yorodumi
- PDB-3pbc: Peptidase module of the peptidoglycan hydrolase RipA (Rv1477) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pbc
TitlePeptidase module of the peptidoglycan hydrolase RipA (Rv1477) from Mycobacterium tuberculosis at 1.38 resolution
ComponentsINVASION PROTEIN
KeywordsHYDROLASE / petidoglycan / cell wall / extracellular / peptidoglycan hydrolase / NlpC -like module
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 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan endopeptidase RipA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsSchnell, R. / Both, D. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Peptidoglycan Remodeling in Mycobacterium tuberculosis: Comparison of Structures and Catalytic Activities of RipA and RipB.
Authors: Both, D. / Schneider, G. / Schnell, R.
History
DepositionOct 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INVASION PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,6081
Polymers22,6081
Non-polymers00
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.797, 66.431, 68.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein INVASION PROTEIN


Mass: 22607.654 Da / Num. of mol.: 1 / Fragment: unp residues 260-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1477 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53168
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.84 Å3/Da / Density % sol: 33.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulphate, 0.1M Tris HCl pH 8.5, 35%w/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2009 / Details: mirrors
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.38→66.4 Å / Num. all: 16683 / Num. obs: 16433 / % possible obs: 98.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 12.9
Reflection shellResolution: 1.38→1.416 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3 / Num. unique all: 4569 / Rsym value: 0.381 / % possible all: 83.94

-
Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→66.4 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.845 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16662 1730 5 %RANDOM
Rwork0.11989 ---
obs0.12227 16433 98.28 %-
all-32788 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.056 Å0.058 Å
Refinement stepCycle: LAST / Resolution: 1.38→66.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 0 264 1807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221636
X-RAY DIFFRACTIONr_bond_other_d0.0010.021128
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9722238
X-RAY DIFFRACTIONr_angle_other_deg1.06432753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80422.65664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.52715258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5071514
X-RAY DIFFRACTIONr_chiral_restr0.1280.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_mcbond_it2.1321.51052
X-RAY DIFFRACTIONr_mcbond_other0.9341.5439
X-RAY DIFFRACTIONr_mcangle_it2.96421702
X-RAY DIFFRACTIONr_scbond_it4.0753584
X-RAY DIFFRACTIONr_scangle_it5.6244.5527
X-RAY DIFFRACTIONr_rigid_bond_restr1.9732764
X-RAY DIFFRACTIONr_sphericity_free12.3023265
X-RAY DIFFRACTIONr_sphericity_bonded4.25632719
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 91 -
Rwork0.169 2068 -
obs-2068 83.94 %

+
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