[English] 日本語
Yorodumi
- PDB-5mor: Joint X-ray/neutron structure of cationic trypsin in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mor
TitleJoint X-ray/neutron structure of cationic trypsin in complex with benzylamine
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
DEUTERATED WATER / (phenylmethyl)azanium / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsSchiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind
CitationJournal: to be published
Title: Joint X-ray/neutron structure of cationic trypsin in complex with benzylamine
Authors: Schiebel, J. / Heine, A. / Klebe, G.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 1, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7616
Polymers23,3241
Non-polymers4365
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17330 Å2
ΔGint4 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.841, 58.334, 67.781
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 (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-UFZ / (phenylmethyl)azanium / Benzylamine


Mass: 108.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: D2O

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 15.0-16.5% (w/v) PEG 8000

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
22951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)10.8266
NUCLEAR REACTORFRM II BIODIFF22.673
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJun 10, 2015
MAATEL BIODIFF2IMAGE PLATEAug 10, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.82661
22.6731
Reflection

Entry-ID: 5MOR

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
0.98-44.21512457999.66.4030.052119.99
1.49-503402293.72.80.12925.866
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
0.98-1.046.1840.5624.18198.7
1.49-1.522.10.4451.954290.4

-
Processing

Software
NameVersionClassification
PHENIX(dev_2429)refinement
XDSdata reduction
HKL-2000data reduction
XDSdata scaling
HKL-2000data scaling
PHASERphasing
Cootmodel building
Refinement

SU ML: 0.06 / R Free selection details: Random selection / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 7.89 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4I8H

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
0.98-17.437X-RAY DIFFRACTION0.10770.09950.099962421244845.0199.6111.36
1.49-19.667NEUTRON DIFFRACTION0.20740.19620.19681713340045.0493.672
Refinement stepCycle: LAST / Resolution: 0.98→17.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 24 146 1783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063746
X-RAY DIFFRACTIONf_angle_d1.2616426
X-RAY DIFFRACTIONf_dihedral_angle_d14.535975
X-RAY DIFFRACTIONf_chiral_restr0.098279
X-RAY DIFFRACTIONf_plane_restr0.008794
NEUTRON DIFFRACTIONf_bond_d0.0063746
NEUTRON DIFFRACTIONf_angle_d1.2616426
NEUTRON DIFFRACTIONf_dihedral_angle_d14.535975
NEUTRON DIFFRACTIONf_chiral_restr0.098279
NEUTRON DIFFRACTIONf_plane_restr0.008794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.99120.20961990.20453718X-RAY DIFFRACTION95
0.9912-1.00280.19932250.19143860X-RAY DIFFRACTION100
1.0028-1.01510.18692020.17463917X-RAY DIFFRACTION100
1.0151-1.02790.14532160.15443913X-RAY DIFFRACTION100
1.0279-1.04140.16012110.13563880X-RAY DIFFRACTION100
1.0414-1.05570.12682260.12333902X-RAY DIFFRACTION100
1.0557-1.07080.11971980.11143903X-RAY DIFFRACTION100
1.0708-1.08670.10711980.10343889X-RAY DIFFRACTION100
1.0867-1.10370.09621970.09213947X-RAY DIFFRACTION100
1.1037-1.12180.10921970.08313903X-RAY DIFFRACTION100
1.1218-1.14120.10532180.07733932X-RAY DIFFRACTION100
1.1412-1.16190.08482250.0733888X-RAY DIFFRACTION100
1.1619-1.18420.08351880.07423908X-RAY DIFFRACTION100
1.1842-1.20840.0932150.07143946X-RAY DIFFRACTION100
1.2084-1.23470.08771860.07263922X-RAY DIFFRACTION100
1.2347-1.26340.08672110.06993945X-RAY DIFFRACTION100
1.2634-1.2950.08641880.07173949X-RAY DIFFRACTION100
1.295-1.330.07882060.06913932X-RAY DIFFRACTION100
1.33-1.36910.08392030.07113935X-RAY DIFFRACTION100
1.3691-1.41330.08021950.07093968X-RAY DIFFRACTION100
1.4133-1.46380.07852170.06953935X-RAY DIFFRACTION100
1.4638-1.52230.07732360.0673944X-RAY DIFFRACTION100
1.5223-1.59160.08322180.07033931X-RAY DIFFRACTION100
1.5916-1.67540.07982160.0713981X-RAY DIFFRACTION100
1.6754-1.78030.07811910.0764011X-RAY DIFFRACTION100
1.7803-1.91760.08242330.08213930X-RAY DIFFRACTION100
1.9176-2.11030.09422230.08524018X-RAY DIFFRACTION100
2.1103-2.4150.11032080.09624021X-RAY DIFFRACTION100
2.415-3.040.13051900.12494083X-RAY DIFFRACTION100
3.04-17.43970.13862060.1344231X-RAY DIFFRACTION100
1.4886-1.53230.28541550.29712503NEUTRON DIFFRACTION89
1.5323-1.58180.2751430.2632667NEUTRON DIFFRACTION95
1.5818-1.63830.23731440.24812739NEUTRON DIFFRACTION96
1.6383-1.70380.24691500.23042759NEUTRON DIFFRACTION97
1.7038-1.78130.2561370.22052797NEUTRON DIFFRACTION98
1.7813-1.87520.20821530.20452760NEUTRON DIFFRACTION97
1.8752-1.99260.21351630.18772757NEUTRON DIFFRACTION97
1.9926-2.14620.18951420.18042725NEUTRON DIFFRACTION95
2.1462-2.36190.20241270.18852359NEUTRON DIFFRACTION82
2.3619-2.70290.18291330.16552564NEUTRON DIFFRACTION89
2.7029-3.40250.17511250.16462756NEUTRON DIFFRACTION93
3.4025-19.66890.15941410.15842905NEUTRON DIFFRACTION95

+
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