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- PDB-6twc: Crystal Structure of the Catalytic Domain of the Coagulation Fact... -

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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 XIFactor 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 / membrane / identical protein binding / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...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 / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
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

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Components

#1: Protein Coagulation factor XI / 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 / 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 / Acetone


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

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Experimental details

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Experiment

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

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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

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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

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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

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