[English] 日本語
Yorodumi
- PDB-6twc: Crystal Structure of the Catalytic Domain of the Coagulation Fact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6twc
TitleCrystal Structure of the Catalytic Domain of the Coagulation Factor XIa in Complex with Double Bridged Peptide F21
Components
  • (Coagulation factor XI) x 2
  • Double Bridged Peptide F21
KeywordsBLOOD CLOTTING / Protease / Coagulation factors / Inhibitor / Double bridged peptide / Phage display
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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 ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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
ACETONE / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsKong, X.D. / Pojer, F. / Heinis, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation157842 Switzerland
CitationJournal: Nat Biomed Eng / Year: 2020
Title: De novo development of proteolytically resistant therapeutic peptides for oral administration.
Authors: Kong, X.D. / Moriya, J. / Carle, V. / Pojer, F. / Abriata, L.A. / Deyle, K. / Heinis, C.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coagulation factor XI
H: Coagulation factor XI
C: Double Bridged Peptide F21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3055
Polymers31,1893
Non-polymers1162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-7 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.162, 76.162, 117.078
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Coagulation factor XI / FXI / Plasma thromboplastin antecedent / PTA


Mass: 27600.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Escherichia coli (E. coli) / References: UniProt: P03951, coagulation factor XIa
#2: Protein/peptide Coagulation factor XI / FXI / Plasma thromboplastin antecedent / PTA


Mass: 2159.419 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Escherichia coli (E. coli) / References: UniProt: P03951, coagulation factor XIa
#3: Protein/peptide Double Bridged Peptide F21


Mass: 1428.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ACN / ACETONE


Mass: 58.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 200 mM (NH4)2SO4, 25% PEG4000, and 100 mM NaOAc, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→43.783 Å / Num. obs: 9502 / % possible obs: 99.6 % / Redundancy: 12.301 % / Biso Wilson estimate: 56.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.13 / Χ2: 1.053 / Net I/σ(I): 22.33 / Num. measured all: 116888
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.86-3.0311.5310.9743.2617216151214930.9631.01998.7
3.03-3.2412.7990.5256.617868140013960.9810.54799.7
3.24-3.512.260.27111.2216245133013250.9950.28399.6
3.5-3.8313.1590.18916.9816199123212310.9970.19799.9
3.83-4.2712.8210.11426.0414206111011080.9990.11899.8
4.27-4.9312.3350.07436.72121509879850.9990.07799.8
4.93-6.0211.5890.06238.55100018638630.9990.065100
6.02-8.4311.8820.04848.3581396856850.9990.05100
8.43-43.78311.6920.02974.4548644214160.9990.0398.8

-
Processing

Software
NameVersionClassification
PHENIXdev-3374refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TY6

4ty6


Resolution: 2.86→43.782 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 508 5.37 %
Rwork0.2131 8953 -
obs0.2156 9461 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.95 Å2 / Biso mean: 67.8712 Å2 / Biso min: 43.23 Å2
Refinement stepCycle: final / Resolution: 2.86→43.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 8 0 2046
Biso mean--65.42 --
Num. residues----258
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.86-3.14780.34281170.2828218799
3.1478-3.60310.32031310.2268218699
3.6031-4.53880.23981120.19612245100
4.5388-43.7820.22991480.20282335100

+
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