[English] 日本語
Yorodumi
- PDB-6zfj: Trypsin inhibitor in complex with bovine trypsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zfj
TitleTrypsin inhibitor in complex with bovine trypsin
ComponentsCationic trypsin
KeywordsHYDROLASE / Fragment / protease / Serine protease
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
1H-isoindol-3-amine / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsBadran, M.J. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Trypsin inhibitor in complex with bovine trypsin
Authors: Badran, M.J. / Heine, A. / Klebe, G.
History
DepositionJun 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 24, 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)24,0199
Polymers23,3241
Non-polymers6958
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-36 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.325, 58.210, 66.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#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

-
Non-polymers , 5 types, 286 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-F05 / 1H-isoindol-3-amine


Mass: 132.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.3 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: ammonium sulfat PEG8000 ethylene glycol HEPES / PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 19, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 113783 / % possible obs: 99.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 6.14 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.73
Reflection shellResolution: 1→1.06 Å / Num. unique obs: 18318 / CC1/2: 0.99

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MNK

5mnk


Resolution: 1→43.9 Å / SU ML: 0.0381 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 8.6807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1261 5689 5 %
Rwork0.1133 108092 -
obs0.1139 113781 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.57 Å2
Refinement stepCycle: LAST / Resolution: 1→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 38 278 1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591894
X-RAY DIFFRACTIONf_angle_d1.03032601
X-RAY DIFFRACTIONf_chiral_restr0.0886282
X-RAY DIFFRACTIONf_plane_restr0.0078351
X-RAY DIFFRACTIONf_dihedral_angle_d14.817698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.10761880.10043569X-RAY DIFFRACTION99.47
1.01-1.020.11361890.09373592X-RAY DIFFRACTION99.6
1.02-1.040.11031880.09413575X-RAY DIFFRACTION99.81
1.04-1.050.10731890.09133605X-RAY DIFFRACTION99.53
1.05-1.060.10581880.09053571X-RAY DIFFRACTION98.97
1.06-1.080.10881840.08983493X-RAY DIFFRACTION97.46
1.08-1.090.09951890.08743587X-RAY DIFFRACTION99.79
1.09-1.110.10041890.08673601X-RAY DIFFRACTION99.76
1.11-1.130.11121880.08883569X-RAY DIFFRACTION99.73
1.13-1.140.11091900.08793603X-RAY DIFFRACTION99.45
1.14-1.160.08791890.08553599X-RAY DIFFRACTION99.37
1.16-1.190.11461880.09063567X-RAY DIFFRACTION99.08
1.19-1.210.09721860.09293535X-RAY DIFFRACTION97.77
1.21-1.230.0991860.09493535X-RAY DIFFRACTION97.74
1.23-1.260.10631890.09733584X-RAY DIFFRACTION99.6
1.26-1.290.10981890.09973603X-RAY DIFFRACTION99.37
1.29-1.320.12151890.10383589X-RAY DIFFRACTION99.24
1.32-1.360.11241900.10173605X-RAY DIFFRACTION99.35
1.36-1.40.11571890.10463585X-RAY DIFFRACTION98.87
1.4-1.440.12461880.10263577X-RAY DIFFRACTION98.51
1.44-1.490.11491870.1053551X-RAY DIFFRACTION97.57
1.49-1.550.11611900.10593617X-RAY DIFFRACTION99.35
1.55-1.620.12821920.10993635X-RAY DIFFRACTION99.4
1.62-1.710.12151900.10723612X-RAY DIFFRACTION99.19
1.71-1.820.12991920.11143648X-RAY DIFFRACTION99.35
1.82-1.960.12841890.11223602X-RAY DIFFRACTION98.52
1.96-2.150.10681910.11233632X-RAY DIFFRACTION98.2
2.15-2.470.15281940.12063681X-RAY DIFFRACTION99.41
2.47-3.110.14851950.13983706X-RAY DIFFRACTION99.44
3.11-43.90.16222040.15583864X-RAY DIFFRACTION98.74

+
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