[English] 日本語
Yorodumi
- PDB-2pkc: CRYSTAL STRUCTURE OF CALCIUM-FREE PROTEINASE K AT 1.5 ANGSTROMS R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pkc
TitleCRYSTAL STRUCTURE OF CALCIUM-FREE PROTEINASE K AT 1.5 ANGSTROMS RESOLUTION
ComponentsPROTEINASE K
KeywordsHYDROLASE(SERINE PROTEINASE)
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / 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 ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsMueller, A. / Hinrichs, W. / Wolf, W.M. / Saenger, W.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Crystal structure of calcium-free proteinase K at 1.5-A resolution.
Authors: Muller, A. / Hinrichs, W. / Wolf, W.M. / Saenger, W.
#1: Journal: Nature / Year: 1989
Title: Long-Range Structural Changes in Proteinase K Triggered by Calcium Ion Removal
Authors: Bajorath, J. / Raghunathan, S. / Hinrichs, W. / Saenger, W.
#2: Journal: Eur.J.Biochem. / Year: 1986
Title: Three-Dimensional Structure of Proteinase K at 0.15-Nm Resolution
Authors: Betzel, C. / Pal, G.P. / Saenger, W.
History
DepositionJun 4, 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: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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: PROTEINASE K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9542
Polymers28,9311
Non-polymers231
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.270, 68.270, 108.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 171
2: RESIDUES SER 15, SER 219, AND SER 247, SHOWED TWOFOLD DISORDERED POSITIONS FOR ATOM OG, HENCE THEIR ALTERNATE INDICATORS ARE *A* AND *B*. THEY HAVE AN OCCUPANCY OF 0.5 EACH, AND WERE REFINED AS DESCRIBED ABOVE.
3: ONE WATER (HOH 322) WAS LOCATED PRECISELY ON AN ELEMENT OF SYMMETRY, THEREFORE, IT WAS GIVEN HALF THE OCCUPANCY IT WOULD HAVE HAD, IF NOT LOCATED ON THE AXIS (OCC.=0.35).
4: ALL ATOMS OF THE PEPTIDE SEQUENCE WERE LOCATED, EXCEPT FOR THE SIDE-CHAIN OF THE C-TERMINAL GLN (278), WHICH WAS ONLY FOUND UP TO CB.
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

-
Components

#1: Protein PROTEINASE K


Mass: 28930.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE ARE THREE BENDS IN THIS STRUCTURE. S1: SER 79, GLY 83; S2: TRP 212, SER 216 (NESTED WITH T16); ...THERE ARE THREE BENDS IN THIS STRUCTURE. S1: SER 79, GLY 83; S2: TRP 212, SER 216 (NESTED WITH T16); S3: THR 244, ALA 248.
Has protein modificationY
Sequence detailsTHE PROTEIN SEQUENCE (279 AMINO ACIDS) IS THE SAME AS THAT OF THE NATIVE ENZYME PRESENTED IN ...THE PROTEIN SEQUENCE (279 AMINO ACIDS) IS THE SAME AS THAT OF THE NATIVE ENZYME PRESENTED IN PROTEIN DATA BANK ENTRY 2PRK.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 %(w/v)protein1drop
250 mMTris-HCl1drop
3300 mMsodium-EDTA1drop
40.02 %1dropNaN3
50.75 M1reservoirNaNO3

-
Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. obs: 33854 / % possible obs: 78 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.147

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.201 / Highest resolution: 1.5 Å
Details: THE OCCUPANCIES OF WATER OXYGENS COULD BE REFINED IN A LAST CYCLE OF REFINEMENT, BUT ONLY THOSE WITH OCCUPANCY GREATER THAN 0.5 WERE RETAINED.
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 1 194 2224
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor obs: 0.201
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