[English] 日本語
Yorodumi
- PDB-1stf: THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1stf
TitleTHE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION
Components
  • PAPAIN
  • STEFIN B (CYSTATIN B)
KeywordsHYDROLASE(SULFHYDRYL PROTEINASE)
Function / homology
Function and homology information


papain / endopeptidase inhibitor activity / serpin family protein binding / cysteine-type endopeptidase inhibitor activity / negative regulation of proteolysis / cysteine-type peptidase activity / adult locomotory behavior / tertiary granule lumen / : / protease binding ...papain / endopeptidase inhibitor activity / serpin family protein binding / cysteine-type endopeptidase inhibitor activity / negative regulation of proteolysis / cysteine-type peptidase activity / adult locomotory behavior / tertiary granule lumen / : / protease binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / nucleolus / proteolysis / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesCarica papaya (papaya)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.37 Å
AuthorsStubbs, M.T. / Laber, B. / Bode, W.
Citation
Journal: EMBO J. / Year: 1990
Title: The refined 2.4 A X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction.
Authors: Stubbs, M.T. / Laber, B. / Bode, W. / Huber, R. / Jerala, R. / Lenarcic, B. / Turk, V.
#1: Journal: FEBS Lett. / Year: 1991
Title: Minireview: The Cystatins: Protein Inhibitors of Cysteine Proteinases
Authors: Turk, V. / Bode, W.
#2: Journal: Biol.Chem.Hoppe-Seyler / Year: 1990
Title: Mutations in the Qvvag Region of the Cysteine Proteinase Inhibitor Stefin B
Authors: Jerala, R. / Trstenjak-Prebanda, M. / Kroon-Zitko, L. / Lenarcic, B. / Turk, V.
History
DepositionApr 21, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: PAPAIN
I: STEFIN B (CYSTATIN B)


Theoretical massNumber of molelcules
Total (without water)34,6812
Polymers34,6812
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-12 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.000, 67.000, 169.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO E 152
2: VAL I 66 - GLY I 67 OMEGA =214.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

-
Components

#1: Protein PAPAIN


Mass: 23507.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carica papaya (papaya) / Organ: FRUIT / Production host: Escherichia coli (E. coli) / References: UniProt: P00784, papain
#2: Protein STEFIN B (CYSTATIN B)


Mass: 11173.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: FRUIT / Production host: Escherichia coli (E. coli) / References: UniProt: P04080
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG15501reservoir
20.75 Mphosphate1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2.37 Å / Num. obs: 16084 / % possible obs: 89 % / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 2.44 Å

-
Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2.37→8 Å /
RfactorNum. reflection
Rwork0.19 -
obs-16033
Refinement stepCycle: LAST / Resolution: 2.37→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 4 142 2590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.1
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 8 Å / Num. reflection obs: 16033 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.1

+
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