[English] 日本語
Yorodumi
- PDB-4i0w: Structure of the Clostridium Perfringens CspB protease -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i0w
TitleStructure of the Clostridium Perfringens CspB protease
Components(Protease CspB) x 2
KeywordsHYDROLASE / jellyroll / subtilisin
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / serine-type endopeptidase activity
Similarity search - Function
Jelly Rolls - #1290 / Alpha-Beta Plaits - #2980 / Peptidase S8A, subtilisin-related, clostridia / Csp protease B, prodomain / Csp protease B prodomain / CspA-like domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. ...Jelly Rolls - #1290 / Alpha-Beta Plaits - #2980 / Peptidase S8A, subtilisin-related, clostridia / Csp protease B, prodomain / Csp protease B prodomain / CspA-like domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Jelly Rolls / Alpha-Beta Plaits / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protease CspB / Protease CspB
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsAdams, C.M. / Eckenroth, B.E. / Doublie, S.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural and functional analysis of the CspB protease required for Clostridium spore germination.
Authors: Adams, C.M. / Eckenroth, B.E. / Putnam, E.E. / Doublie, S. / Shen, A.
History
DepositionNov 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease CspB
B: Protease CspB
C: Protease CspB
D: Protease CspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,07117
Polymers127,4224
Non-polymers64913
Water17,042946
1
A: Protease CspB
B: Protease CspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9918
Polymers63,7112
Non-polymers2806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-43 kcal/mol
Surface area21980 Å2
MethodPISA
2
C: Protease CspB
D: Protease CspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0809
Polymers63,7112
Non-polymers3697
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-28 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.876, 138.112, 140.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Protease CspB


Mass: 10855.533 Da / Num. of mol.: 2 / Fragment: prodomain (UNP residues 1-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CPF_2887, cspB / Plasmid: pRSFduet1-cspB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0TM89, UniProt: A0A0H2YU83*PLUS, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Protease CspB


Mass: 52855.551 Da / Num. of mol.: 2 / Fragment: subtilase domain (UNP residues 97-565)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CPF_2887, cspB / Plasmid: pRSFduet1-cspB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0TM89, UniProt: A0A0H2YU83*PLUS, Hydrolases; Acting on peptide bonds (peptidases)

-
Non-polymers , 4 types, 959 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 946 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 27% ethylene glycol, 50 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2012
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.49→43.735 Å / Num. all: 202733 / Num. obs: 202733 / % possible obs: 86.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.419
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.05 / % possible all: 46.2

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.6→43.735 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.35 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1809 17844 9.99 %
Rwork0.1618 --
obs0.1637 178612 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.4632 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8626 0 37 946 9609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078991
X-RAY DIFFRACTIONf_angle_d0.80312231
X-RAY DIFFRACTIONf_dihedral_angle_d11.2133301
X-RAY DIFFRACTIONf_chiral_restr0.0581391
X-RAY DIFFRACTIONf_plane_restr0.0041588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.22984420.18213904X-RAY DIFFRACTION70
1.6182-1.63720.21284200.17354063X-RAY DIFFRACTION72
1.6372-1.65720.22314830.17134265X-RAY DIFFRACTION77
1.6572-1.67820.21664710.16444471X-RAY DIFFRACTION79
1.6782-1.70030.21095300.16934666X-RAY DIFFRACTION84
1.7003-1.72360.20045200.16714887X-RAY DIFFRACTION86
1.7236-1.74820.19545620.16945040X-RAY DIFFRACTION90
1.7482-1.77430.21115340.16175232X-RAY DIFFRACTION92
1.7743-1.8020.19456010.15495360X-RAY DIFFRACTION95
1.802-1.83150.19446480.15385413X-RAY DIFFRACTION98
1.8315-1.86310.17956140.15555580X-RAY DIFFRACTION99
1.8631-1.8970.17625910.15765652X-RAY DIFFRACTION100
1.897-1.93350.17966150.16025647X-RAY DIFFRACTION100
1.9335-1.9730.19496180.15745613X-RAY DIFFRACTION100
1.973-2.01590.18135770.15875695X-RAY DIFFRACTION100
2.0159-2.06270.18826230.15335642X-RAY DIFFRACTION100
2.0627-2.11430.17676730.16215598X-RAY DIFFRACTION100
2.1143-2.17150.19486460.15885607X-RAY DIFFRACTION100
2.1715-2.23540.18556200.15835681X-RAY DIFFRACTION100
2.2354-2.30750.18715970.15515682X-RAY DIFFRACTION100
2.3075-2.390.186460.15765630X-RAY DIFFRACTION100
2.39-2.48570.18566670.16125615X-RAY DIFFRACTION100
2.4857-2.59880.1966400.17095650X-RAY DIFFRACTION100
2.5988-2.73580.18796130.16625723X-RAY DIFFRACTION100
2.7358-2.90720.19316220.17435678X-RAY DIFFRACTION100
2.9072-3.13160.1846510.17255692X-RAY DIFFRACTION100
3.1316-3.44660.1856620.16715705X-RAY DIFFRACTION100
3.4466-3.94510.1636300.15915764X-RAY DIFFRACTION100
3.9451-4.96930.14926740.14055752X-RAY DIFFRACTION100
4.9693-43.7510.18096540.17575861X-RAY DIFFRACTION97

+
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