[English] 日本語
Yorodumi
- PDB-2sic: REFINED CRYSTAL STRUCTURE OF THE COMPLEX OF SUBTILISIN BPN' AND S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2sic
TitleREFINED CRYSTAL STRUCTURE OF THE COMPLEX OF SUBTILISIN BPN' AND STREPTOMYCES SUBTILISIN INHIBITOR AT 1.8 ANGSTROMS RESOLUTION
Components
  • STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
  • SUBTILISIN BPN'
KeywordsCOMPLEX (PROTEINASE/INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) complex
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor, conserved site / Streptomyces subtilisin-type inhibitors signature. / Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain ...Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor, conserved site / Streptomyces subtilisin-type inhibitors signature. / Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin BPN' / Subtilisin inhibitor
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsMitsui, Y. / Takeuchi, Y. / Hirono, S. / Akagawa, H. / Nakamura, K.T.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined crystal structure of the complex of subtilisin BPN' and Streptomyces subtilisin inhibitor at 1.8 A resolution.
Authors: Takeuchi, Y. / Satow, Y. / Nakamura, K.T. / Mitsui, Y.
#1: Journal: J.Mol.Biol. / Year: 1984
Title: Crystal Structure at 2.6 Angstroms Resolution of the Complex of Subtilisin with Bpn' with Streptomyces Subtilisin Inhibitor
Authors: Hirono, S. / Akagawa, H. / Mitsui, Y. / Iitaka, Y.
#2: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of the Complex of Subtilisin Bpn' with its Protein Inhibitor Streptomyces Subtilisin Inhibitor
Authors: Hirono, S. / Nakamura, K.T. / Iitaka, Y. / Mitsui, Y.
#3: Journal: Nature / Year: 1979
Title: Crystal Structures of Streptomyces Subtilisin Inhibitor and its Complex with Subtilisin Bpn'
Authors: Mitsui, Y. / Satow, Y. / Watanabe, Y. / Hirono, S. / Iitaka, Y.
History
DepositionApr 1, 1991Processing site: BNL
SupersessionApr 15, 1993ID: 1SIC
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: SUBTILISIN BPN'
I: STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5734
Polymers38,4932
Non-polymers802
Water4,648258
1
E: SUBTILISIN BPN'
I: STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
hetero molecules

E: SUBTILISIN BPN'
I: STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1468
Polymers76,9864
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4880 Å2
ΔGint-37.2 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.230, 185.900, 69.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: RESIDUES PRO E 168 AND PRO I 37 ARE CIS PROLINES.

-
Components

#1: Protein SUBTILISIN BPN'


Mass: 27552.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / References: UniProt: P00782, 3.4.21.14
#2: Protein STREPTOMYCES SUBTILISIN INHIBITOR (SSI)


Mass: 10940.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P01006
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Details: used seeding, Hirono, S., (1979) J.Mol.Biol., 131, 855.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1BPN1150mg
2SSI1117.5mg
30.05 MTris-HCl11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 28118 / Observed criterion σ(F): 2 / Num. measured all: 97766 / Rmerge(I) obs: 0.0472

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å /
RfactorNum. reflection
obs0.177 26760
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 2 258 2962
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.017
X-RAY DIFFRACTIONp_angle_d0.0340.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.037
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.110.1
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.82.5
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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