[English] 日本語
Yorodumi
- PDB-1sio: Structure of Kumamolisin-As complexed with a covalently-bound inh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sio
TitleStructure of Kumamolisin-As complexed with a covalently-bound inhibitor, AcIPF
Components
  • Ace-ILE-PRO-PHL peptide inhibitor
  • kumamolisin-As
KeywordsHYDROLASE/HYDROLASE INHIBITOR / KUMAMOLISIN-AS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


tripeptidyl-peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain ...Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal / : / Kumamolisin-As
Similarity search - Component
Biological speciesAlicyclobacillus sendaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, M. / Wlodawer, A. / Gustchina, A. / Tsuruoka, N. / Ashida, M. / Minakata, H. / Oyama, H. / Oda, K. / Nishino, T. / Nakayama, T.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity
Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Tsuruoka, N. / Ashida, M. / Minakata, H. / Oyama, H. / Oda, K. / Nishino, T. / Nakayama, T.
History
DepositionMar 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: kumamolisin-As
B: kumamolisin-As
C: kumamolisin-As
D: Ace-ILE-PRO-PHL peptide inhibitor
E: Ace-ILE-PRO-PHL peptide inhibitor
F: Ace-ILE-PRO-PHL peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,72612
Polymers111,3186
Non-polymers4086
Water16,844935
1
A: kumamolisin-As
D: Ace-ILE-PRO-PHL peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2424
Polymers37,1062
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: kumamolisin-As
E: Ace-ILE-PRO-PHL peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2424
Polymers37,1062
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-39 kcal/mol
Surface area12790 Å2
MethodPISA
3
C: kumamolisin-As
F: Ace-ILE-PRO-PHL peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2424
Polymers37,1062
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-30 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.370, 238.730, 49.250
Angle α, β, γ (deg.)90.00, 113.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein kumamolisin-As


Mass: 36718.359 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus sendaiensis (bacteria)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 25900987, UniProt: Q8GB88*PLUS
#2: Protein/peptide Ace-ILE-PRO-PHL peptide inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 387.516 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNBOUND INHIBITOR (CHAIN D/E/F) IS ACE-ILE-PRO-PHA, N-ACETYL-L-ISOLEUCYL-L-PROLYL-L- ...THE UNBOUND INHIBITOR (CHAIN D/E/F) IS ACE-ILE-PRO-PHA, N-ACETYL-L-ISOLEUCYL-L-PROLYL-L-PHENYLALANINE WITH C-TERMINAL PHENYLALANINAL. UPON REACTION THE INHIBITOR COVALENTLY BINDS TO THE OG ATOM OF SER 278 OF THE ENZYME (CHAIN A/B/C) FORMING A TETRAHEDRAL HEMIACETAL. DUE TO THE CHEMICAL CHANGE, THE C-TERMINAL RESIDUE IS REPRESENTED IN SEQUENCE AS PHL, PHENYLALANINOL

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 8000, Ammonium sulfate, DTT, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9982 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2003
RadiationMonochromator: OSMIC mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99821
21.54181
ReflectionResolution: 1.8→25 Å / Num. all: 93159 / Num. obs: 93159 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.053 / Net I/σ(I): 23
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rsym value: 0.311 / % possible all: 76.8

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GT9

1gt9


Resolution: 1.8→10 Å / Num. parameters: 34499 / Num. restraintsaints: 32199 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 4457 5.3 %RANDOM
all0.1734 89193 --
obs0.173 84178 88.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 8621
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7668 0 18 935 8621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0218
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.075
X-RAY DIFFRACTIONs_approx_iso_adps0

+
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