[English] 日本語
Yorodumi
- PDB-6txg: Proteinase K in complex with a "half sandwich"-type Ru(II) coordi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6txg
TitleProteinase K in complex with a "half sandwich"-type Ru(II) coordination compound
ComponentsProteinase K
KeywordsHYDROLASE / enzyme / complex / anticancer
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/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 / Chem-NYN / trifluoromethanesulfonic acid / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.372 Å
AuthorsChiniadis, L. / Giastas, P. / Bratsos, I. / Papakyriakou, A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: High-resolution crystal structures of a "half sandwich"-type Ru(II) coordination compound bound to hen egg-white lysozyme and proteinase K.
Authors: Chiniadis, L. / Bratsos, I. / Bethanis, K. / Karpusas, M. / Giastas, P. / Papakyriakou, A.
History
DepositionJan 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,15711
Polymers28,9591
Non-polymers1,19810
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-16 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.708, 67.708, 107.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-634-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K

-
Non-polymers , 7 types, 277 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NYN / chlorido(1,2-diaminoethane-k2N,N')(1,4,7-trithiacyclononane-k3S,S',S'')ruthenium(II) trifluoromethanesulfonate


Mass: 337.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16N2RuS3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TFS / trifluoromethanesulfonic acid


Mass: 150.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHF3O3S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1M SODIUM NITRATE, 0.1M CITRATE BUFFER, pH=6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.372→57.263 Å / Num. obs: 99661 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01091 / Rpim(I) all: 0.01091 / Rrim(I) all: 0.01544 / Net I/σ(I): 34.91
Reflection shellResolution: 1.372→1.421 Å / Rmerge(I) obs: 0.0539 / Num. unique obs: 5186 / CC1/2: 0.992 / CC star: 0.998 / Rpim(I) all: 0.0539 / Rrim(I) all: 0.07622

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ID8

2id8


Resolution: 1.372→57.263 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 14.97
RfactorNum. reflection% reflection
Rfree0.1675 4811 4.83 %
Rwork0.1513 --
obs0.1521 99661 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.16 Å2 / Biso mean: 14.9304 Å2 / Biso min: 6 Å2
Refinement stepCycle: final / Resolution: 1.372→57.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 98 267 2396
Biso mean--27.94 25.54 -
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.372-1.38760.23041670.1883174100
1.3876-1.40390.21981330.17333193100
1.4039-1.42110.17031400.16243151100
1.4211-1.4390.18641550.16453223100
1.439-1.4580.19571460.15943158100
1.458-1.4780.18251560.15463169100
1.478-1.49910.16841700.15293169100
1.4991-1.52140.20211480.15253115100
1.5214-1.54520.16911510.15673240100
1.5452-1.57060.19281630.14933124100
1.5706-1.59760.16171630.1423161100
1.5976-1.62670.16552030.14653122100
1.6267-1.6580.15731530.15133160100
1.658-1.69180.16831490.1463223100
1.6918-1.72860.17891620.14573132100
1.7286-1.76880.17251680.14783143100
1.7688-1.81310.1711880.15183134100
1.8131-1.86210.12911610.14693143100
1.8621-1.91690.15041560.15083201100
1.9169-1.97880.19321740.14943124100
1.9788-2.04950.15911660.14783181100
2.0495-2.13150.15431540.14793153100
2.1315-2.22860.15321740.14093135100
2.2286-2.34610.18551690.15373157100
2.3461-2.49310.19241600.15323157100
2.4931-2.68550.16041590.15573144100
2.6855-2.95580.17371240.16473218100
2.9558-3.38350.17431750.15453142100
3.3835-4.26260.13431630.13413144100
4.2626-57.2630.16321610.1556316099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82120.2099-0.09391.21510.14940.74040.0149-0.1870.01820.058-0.0044-0.0909-0.00540.106-0.01390.0581-0.0014-0.00850.1265-0.00040.057920.791815.871831.9699
21.54491.06770.57252.78651.56012.6102-0.00940.04-0.1012-0.12480.0318-0.09250.01570.0612-0.02080.04450.02590.00620.06960.00980.061618.4518.188922.2174
34.8967-0.00051.82915.8999-4.27753.96950.09-0.17150.02530.0883-0.05540.0742-0.0222-0.0732-0.07920.0662-0.00750.00410.0681-0.01430.08424.73492.000824.1145
41.08230.6987-0.28191.4577-0.39490.8510.00720.00010.1028-0.04960.01590.09730.0134-0.0259-0.01480.0520.0075-0.00540.0652-0.00330.05855.36318.56222.5866
51.53070-0.69610.7858-0.20211.07050.0005-0.05480.0474-0.0149-0.0224-0.01890.01010.04580.01390.0553-0.0043-0.00860.0705-0.00830.054619.00718.037625.3853
61.1594-0.1557-1.5378.3748-3.67164.5472-0.033-0.22960.17880.0824-0.01640.3187-0.043-0.08670.04240.0463-0.00490.01990.1336-0.03530.10214.120519.939538.3
72.6797-1.74581.92433.5321-3.07545.8389-0.0724-0.22730.44510.23230.0393-0.0874-0.3921-0.01220.11480.099-0.00720.02160.0959-0.06170.16299.027131.635731.4183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )A1 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 103 )A59 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 120 )A104 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 204 )A121 - 204
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 239 )A205 - 239
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 254 )A240 - 254
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 279 )A255 - 279

+
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://pdbjlvh1.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