[English] 日本語
Yorodumi
- PDB-5mne: Cationic trypsin in its apo form (deuterated sample at 100 K) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mne
TitleCationic trypsin in its apo form (deuterated sample at 100 K)
ComponentsCationic trypsin
KeywordsHYDROLASE / hydrogen bonding / protonation / protein-ligand interaction
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.008 Å
AuthorsSchiebel, J. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind
CitationJournal: Nat Commun / Year: 2018
Title: Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.
Authors: Schiebel, J. / Gaspari, R. / Wulsdorf, T. / Ngo, K. / Sohn, C. / Schrader, T.E. / Cavalli, A. / Ostermann, A. / Heine, A. / Klebe, G.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7496
Polymers23,3241
Non-polymers4245
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-56 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.669, 58.290, 66.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 18-20% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7069 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7069 Å / Relative weight: 1
ReflectionResolution: 1.008→42.322 Å / Num. obs: 110736 / % possible obs: 97.8 % / Redundancy: 6.607 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 26.34
Reflection shellResolution: 1.008→1.01 Å / Redundancy: 6.649 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3.3 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8H

4i8h


Resolution: 1.008→24.748 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 9.57
RfactorNum. reflection% reflectionSelection details
Rfree0.1248 5532 5 %Random selection
Rwork0.1059 ---
obs0.1068 110662 97.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.008→24.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 21 331 1975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091916
X-RAY DIFFRACTIONf_angle_d1.1562645
X-RAY DIFFRACTIONf_dihedral_angle_d13.097712
X-RAY DIFFRACTIONf_chiral_restr0.098286
X-RAY DIFFRACTIONf_plane_restr0.009352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0076-1.0190.21411620.20633091X-RAY DIFFRACTION88
1.019-1.0310.20171790.17423393X-RAY DIFFRACTION95
1.031-1.04360.18331820.1573451X-RAY DIFFRACTION97
1.0436-1.05680.16511800.14583420X-RAY DIFFRACTION97
1.0568-1.07070.15131820.13343451X-RAY DIFFRACTION97
1.0707-1.08540.15751830.12383482X-RAY DIFFRACTION98
1.0854-1.10090.14441820.11513460X-RAY DIFFRACTION98
1.1009-1.11730.12721830.10063475X-RAY DIFFRACTION98
1.1173-1.13480.1181840.09463491X-RAY DIFFRACTION98
1.1348-1.15340.11051830.08983491X-RAY DIFFRACTION98
1.1534-1.17330.10581840.09133492X-RAY DIFFRACTION98
1.1733-1.19460.10361840.09093484X-RAY DIFFRACTION98
1.1946-1.21760.10781850.09413514X-RAY DIFFRACTION98
1.2176-1.24240.12161830.09253489X-RAY DIFFRACTION98
1.2424-1.26940.11361860.08863530X-RAY DIFFRACTION98
1.2694-1.2990.11561820.09143447X-RAY DIFFRACTION98
1.299-1.33140.1171860.0913527X-RAY DIFFRACTION98
1.3314-1.36740.11761820.08743463X-RAY DIFFRACTION97
1.3674-1.40770.10521820.08753470X-RAY DIFFRACTION97
1.4077-1.45310.10891860.08213541X-RAY DIFFRACTION99
1.4531-1.5050.0831850.07943524X-RAY DIFFRACTION99
1.505-1.56530.09971880.08183565X-RAY DIFFRACTION99
1.5653-1.63650.09861870.08353557X-RAY DIFFRACTION99
1.6365-1.72280.10191890.0893573X-RAY DIFFRACTION99
1.7228-1.83070.11121880.09923598X-RAY DIFFRACTION99
1.8307-1.9720.12531890.10173596X-RAY DIFFRACTION99
1.972-2.17030.12841900.10293622X-RAY DIFFRACTION100
2.1703-2.48410.12311870.11013574X-RAY DIFFRACTION98
2.4841-3.12870.13991910.12283624X-RAY DIFFRACTION99
3.1287-24.75590.13951980.12093735X-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