[English] 日本語
Yorodumi
- PDB-1srp: STRUCTURAL ANALYSIS OF SERRATIA PROTEASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1srp
TitleSTRUCTURAL ANALYSIS OF SERRATIA PROTEASE
ComponentsSERRALYSIN
KeywordsHYDROLASE (METALLOPROTEASE)
Function / homology
Function and homology information


serralysin / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat ...Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHamada, K. / Hiramatsu, H. / Katsuya, Y. / Hata, Y. / Katsube, Y.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1996
Title: Crystal structure of Serratia protease, a zinc-dependent proteinase from Serratia sp. E-15, containing a beta-sheet coil motif at 2.0 A resolution.
Authors: Hamada, K. / Hata, Y. / Katsuya, Y. / Hiramatsu, H. / Fujiwara, T. / Katsube, Y.
#1: Journal: Photon Factory Activity Report / Year: 1992
Title: Structural Studies of Serratia Protease by X-Ray Analysis
Authors: Hamada, K. / Hiramatsu, H. / Fujiwara, T. / Katsuya, Y. / Hata, Y. / Katsube, Y.
#2: Journal: J.Biochem.(Tokyo) / Year: 1985
Title: Preliminary X-Ray Studies on Serratia Protease
Authors: Katsuya, Y. / Hamada, K. / Hata, Y. / Tanaka, N. / Sato, M. / Katsube, Y. / Katiuchi, K. / Miyata, K.
History
DepositionNov 2, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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_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_ref_seq_dif.details / _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: SERRALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8399
Polymers50,4931
Non-polymers3468
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.140, 150.890, 42.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEVEN CALCIUM IONS, RESIDUES CA 911 - CA 917, ARE LIGATED TO THE PROTEIN.

-
Components

#1: Protein SERRALYSIN /


Mass: 50493.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. (bacteria) / Strain: E-15 / References: UniProt: P07268, serralysin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal
*PLUS
Density % sol: 67 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme11
22 %(w/v)PEG800011
327 %satammonium sulfate12

-
Data collection

ReflectionNum. obs: 42930 / % possible obs: 88.2 % / Observed criterion σ(I): 0

-
Processing

SoftwareName: GPRLSA / Classification: refinement
RefinementResolution: 2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.184 --
obs0.193 40458 78.6 %
Displacement parametersBiso mean: 18.97 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 8 212 3780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6871
X-RAY DIFFRACTIONp_mcangle_it1.1161.5
X-RAY DIFFRACTIONp_scbond_it0.81
X-RAY DIFFRACTIONp_scangle_it1.3271.5
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1480.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.5
X-RAY DIFFRACTIONp_multtor_nbd0.1990.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1850.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.83
X-RAY DIFFRACTIONp_staggered_tor16.715
X-RAY DIFFRACTIONp_orthonormal_tor28.920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection obs: 38044 / σ(F): 3 / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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