[English] 日本語
Yorodumi
- PDB-4c2d: Crystal structure of the protease CtpB in an active state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c2d
TitleCrystal structure of the protease CtpB in an active state
Components
  • (PEPTIDE2) x 2
  • CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
  • PEPTIDE1
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / PROTEOLYTIC TUNNEL
Function / homology
Function and homology information


C-terminal processing peptidase / peptide metabolic process / sporulation resulting in formation of a cellular spore / peptide binding / peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / serine-type endopeptidase activity / signal transduction / protein homodimerization activity ...C-terminal processing peptidase / peptide metabolic process / sporulation resulting in formation of a cellular spore / peptide binding / peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / serine-type endopeptidase activity / signal transduction / protein homodimerization activity / proteolysis / identical protein binding
Similarity search - Function
: / Activating protease CtpB N-terminal domain / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / PGBD superfamily / PDZ domain ...: / Activating protease CtpB N-terminal domain / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / PGBD superfamily / PDZ domain / PDZ domain / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / PDZ domain / Pdz3 Domain / ClpP/crotonase-like domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Carboxy-terminal processing protease CtpB
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMastny, M. / Heuck, A. / Kurzbauer, R. / Clausen, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Ctpb Assembles a Gated Protease Tunnel Regulating Cell-Cell Signaling During Spore Formation in Bacillus Subtilis.
Authors: Mastny, M. / Heuck, A. / Kurzbauer, R. / Heiduk, A. / Boisguerin, P. / Volkmer, R. / Ehrmann, M. / Rodrigues, C.D.A. / Rudner, D.Z. / Clausen, T.
History
DepositionAug 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
B: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
C: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
D: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
E: PEPTIDE1
F: PEPTIDE1
G: PEPTIDE1
H: PEPTIDE1
M: PEPTIDE2
N: PEPTIDE2
O: PEPTIDE2
P: PEPTIDE2


Theoretical massNumber of molelcules
Total (without water)202,73912
Polymers202,73912
Non-polymers00
Water4,936274
1
A: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
B: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
E: PEPTIDE1
F: PEPTIDE1
M: PEPTIDE2
N: PEPTIDE2


Theoretical massNumber of molelcules
Total (without water)101,3906
Polymers101,3906
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-46.7 kcal/mol
Surface area43770 Å2
MethodPISA
2
C: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
D: CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
G: PEPTIDE1
H: PEPTIDE1
O: PEPTIDE2
P: PEPTIDE2


Theoretical massNumber of molelcules
Total (without water)101,3496
Polymers101,3496
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-47.6 kcal/mol
Surface area39540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.050, 65.375, 169.065
Angle α, β, γ (deg.)90.00, 95.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
CARBOXY-TERMINAL PROCESSING PROTEASE CTPB / C-TERMINAL PROCESSING PROTEASE / CTPB


Mass: 49740.480 Da / Num. of mol.: 4 / Fragment: RESIDUES 44-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: O35002, C-terminal processing peptidase
#2: Protein/peptide
PEPTIDE1


Mass: 518.562 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PEPTIDE CO-PURIFIED FROM E. COLI EXPRESSION / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21
#3: Protein/peptide PEPTIDE2


Mass: 456.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PEPTIDE CO-PURIFIED FROM E. COLI EXPRESSION / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21
#4: Protein/peptide PEPTIDE2


Mass: 415.440 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: PEPTIDE CO-PURIFIED FROM E. COLI EXPRESSION / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.18 Å3/Da / Density % sol: 61.3 % / Description: NONE
Crystal growDetails: 13% PEG 3350, 0.1 M NA-MALONATE, 0.1 M HEPES PH 7.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 79111 / % possible obs: 100 % / Observed criterion σ(I): -10 / Redundancy: 6.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C2C

4c2c


Resolution: 2.7→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 3533 5 %RANDOM
Rwork0.2271 ---
obs0.2271 70464 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.6378 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.358 Å20 Å21.597 Å2
2---14.798 Å20 Å2
3---16.156 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13079 0 0 274 13353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
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