[English] 日本語
Yorodumi
- PDB-6eat: Crystallographic structure of the cyclic nonapeptide derived from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eat
TitleCrystallographic structure of the cyclic nonapeptide derived from the BTCI inhibitor bound to beta-trypsin in space group P 21 21 21.
Components
  • 9MER-PEPTIDE
  • Cationic trypsin
Keywordshydrolase/hydrolase inhibitor / Inhibitor Complex / BTCI / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / : / 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. ...Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / : / 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 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
Serine protease 1 / Horsegram inhibitor 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Vigna unguiculata (cowpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.149 Å
AuthorsFernandes, J.C. / Valadares, N.F. / Freitas, S.M. / Barbosa, J.A.R.G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)309054/2014-1 Brazil
CitationJournal: Arch. Biochem. Biophys. / Year: 2019
Title: Crystallographic structure of a complex between trypsin and a nonapeptide derived from a Bowman-Birk inhibitor found in Vigna unguiculata seeds.
Authors: Fernandes, J.P.C. / Mehdad, A. / Valadares, N.F. / Mourao, C.B.F. / Ventura, M.M. / Barbosa, J.A.R.G. / Freitas, S.M.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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 1.4Nov 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
I: 9MER-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,49415
Polymers24,3012
Non-polymers1,19313
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The assembly has been confirmed by enzymatic activity assays
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-162 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.834, 61.569, 67.030
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: Protein/peptide 9MER-PEPTIDE


Mass: 977.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vigna unguiculata (cowpea) / References: UniProt: Q9S9E3*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes sodium 1 M Monohydrate lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.20011 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 31, 2018
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.20011 Å / Relative weight: 1
ReflectionResolution: 1.149→29.917 Å / Num. obs: 83153 / % possible obs: 94 % / Redundancy: 14 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 1 / Net I/σ(I): 30.21
Reflection shellResolution: 1.149→1.19 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.54 / Num. unique obs: 6078 / CC1/2: 0.651 / % possible all: 69

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RU4

3ru4


Resolution: 1.149→29.917 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.05
RfactorNum. reflection% reflection
Rfree0.1545 2002 2.41 %
Rwork0.1439 --
obs0.1441 83128 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.149→29.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 61 369 2125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0241876
X-RAY DIFFRACTIONf_angle_d1.4532580
X-RAY DIFFRACTIONf_dihedral_angle_d12.59696
X-RAY DIFFRACTIONf_chiral_restr0.091283
X-RAY DIFFRACTIONf_plane_restr0.008323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1493-1.17810.4808900.46063932X-RAY DIFFRACTION64
1.1781-1.20990.29541270.27275090X-RAY DIFFRACTION83
1.2099-1.24550.23261290.21935176X-RAY DIFFRACTION85
1.2455-1.28570.23451370.23095495X-RAY DIFFRACTION90
1.2857-1.33170.16611350.16225695X-RAY DIFFRACTION93
1.3317-1.3850.17761550.15536003X-RAY DIFFRACTION98
1.385-1.4480.15671470.14486113X-RAY DIFFRACTION99
1.448-1.52440.15791500.1416133X-RAY DIFFRACTION100
1.5244-1.61990.15181590.13666152X-RAY DIFFRACTION100
1.6199-1.74490.13721470.13646142X-RAY DIFFRACTION100
1.7449-1.92050.16031540.13256223X-RAY DIFFRACTION100
1.9205-2.19830.13451540.12826201X-RAY DIFFRACTION100
2.1983-2.76930.14931580.13196264X-RAY DIFFRACTION100
2.7693-29.92710.13671600.13396507X-RAY DIFFRACTION100
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)
10.7878-0.2751-0.30791.25390.15311.13760.0091-0.0380.03430.06770.03610.0571-0.01820.0039-0.0450.0938-0.00030.00690.09870.00140.10335.096667.6534148.2681
21.4056-1.6736-0.38595.18090.00721.6435-0.0764-0.00490.03660.0510.04980.03130.117-0.05080.0330.0407-0.0297-0.00940.0847-0.00190.08811.057859.8883144.7556
30.8516-0.1857-0.81031.38660.32031.8434-0.04280.0001-0.0205-0.05180.0346-0.07570.18070.1556-0.00540.09220.01490.01220.09950.00340.080414.892560.2557136.2183
46.75330.9678-1.9151.0508-0.45642.0603-0.17390.07-0.124-0.11790.12620.01770.28840.0130.04890.13740.0073-0.00390.05350.00170.07376.458554.752138.5186
58.4548-0.67282.0476.1045-4.01125.8413-0.0103-0.301-0.14060.2276-0.2477-0.3170.25780.77130.21860.13840.0379-0.00960.18830.01950.096416.736756.3181149.8307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 245 )
5X-RAY DIFFRACTION5chain 'I' and (resid 1 through 9 )

+
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