[English] 日本語
Yorodumi
- PDB-5kxv: Structure Proteinase K at 0.98 Angstroms -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kxv
TitleStructure Proteinase K at 0.98 Angstroms
ComponentsProteinase K
KeywordsHYDROLASE / Serine Protease / hydrolysis / aminolysis / catalytic triad
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Proteinase K-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. ...Proteinase K-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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsMasuda, T. / Suzuki, M. / Inoue, S. / Numata, K. / Sugahara, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology25650026 Japan
CitationJournal: Sci Rep / Year: 2017
Title: Atomic resolution structure of serine protease proteinase K at ambient temperature.
Authors: Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Nakane, T. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Mikami, B. / Nureki, O. / Numata, K. / ...Authors: Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Nakane, T. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Mikami, B. / Nureki, O. / Numata, K. / Iwata, S. / Sugahara, M.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_mutation / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2856
Polymers28,9591
Non-polymers3265
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.577, 67.577, 107.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-706-

HOH

-
Components

#1: Protein Proteinase K / / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH (P2308) / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5 / Details: 250 mM NaNO3, 50 mM CaCl2, 50 mM MES-NaOH

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.98→50 Å / Num. obs: 141433 / % possible obs: 99.5 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 58.41
Reflection shellResolution: 0.98→1 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 6.47 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B5L

4b5l


Resolution: 0.98→16.894 Å / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 7.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.114 6943 4.91 %Random
Rwork0.1002 ---
obs0.1009 141318 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.98→16.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 18 434 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062441
X-RAY DIFFRACTIONf_angle_d0.9673370
X-RAY DIFFRACTIONf_dihedral_angle_d13.485890
X-RAY DIFFRACTIONf_chiral_restr0.08357
X-RAY DIFFRACTIONf_plane_restr0.007468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9802-0.99130.12672080.1374405X-RAY DIFFRACTION99
0.9913-1.0030.15092300.13374391X-RAY DIFFRACTION99
1.003-1.01520.13442320.1194402X-RAY DIFFRACTION99
1.0152-1.0280.1162060.11614452X-RAY DIFFRACTION99
1.028-1.04160.12992460.11124392X-RAY DIFFRACTION99
1.0416-1.05580.1262160.10544456X-RAY DIFFRACTION100
1.0558-1.07090.10932280.10034423X-RAY DIFFRACTION100
1.0709-1.08690.10172400.09364422X-RAY DIFFRACTION100
1.0869-1.10390.09092320.09224409X-RAY DIFFRACTION100
1.1039-1.1220.11082300.0884476X-RAY DIFFRACTION100
1.122-1.14130.09152340.08574430X-RAY DIFFRACTION100
1.1413-1.16210.08822120.08144471X-RAY DIFFRACTION100
1.1621-1.18440.09362530.08084431X-RAY DIFFRACTION100
1.1844-1.20860.09462320.08024492X-RAY DIFFRACTION100
1.2086-1.23480.09352160.08224445X-RAY DIFFRACTION100
1.2348-1.26360.09122320.08554447X-RAY DIFFRACTION100
1.2636-1.29510.11072010.0844539X-RAY DIFFRACTION100
1.2951-1.33020.09772560.08534441X-RAY DIFFRACTION100
1.3302-1.36930.10172220.08514485X-RAY DIFFRACTION100
1.3693-1.41350.11052600.08454484X-RAY DIFFRACTION100
1.4135-1.46390.10222460.08494451X-RAY DIFFRACTION100
1.4639-1.52250.09552440.08124504X-RAY DIFFRACTION100
1.5225-1.59180.09392500.0844488X-RAY DIFFRACTION100
1.5918-1.67560.09472180.08924537X-RAY DIFFRACTION100
1.6756-1.78050.10822450.09474534X-RAY DIFFRACTION100
1.7805-1.91780.12672150.10064527X-RAY DIFFRACTION100
1.9178-2.11050.11742350.0994560X-RAY DIFFRACTION99
2.1105-2.41510.1142120.10444577X-RAY DIFFRACTION99
2.4151-3.03990.12152450.11534567X-RAY DIFFRACTION99
3.0399-16.89680.14222470.12184737X-RAY DIFFRACTION97

+
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