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- PDB-6twb: Crystal Structure of the Catalytic Domain of Coagulation Factor X... -

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Basic information

Entry
Database: PDB / ID: 6twb
TitleCrystal Structure of the Catalytic Domain of Coagulation Factor XIa in Complex with Double Bridged Peptide F19
Components
  • Coagulation factor XI
  • Double Bridged Peptide F19
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 / 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 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
AMMONIUM ION / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.91 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 13, 2020Provider: repository / Type: Initial release
Revision 2.0May 20, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / database_PDB_caveat / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / refine_hist / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine_hist.d_res_high
Revision 2.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XI
H: Coagulation factor XI
B: Double Bridged Peptide F19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7906
Polymers60,7363
Non-polymers543
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-8 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.524, 77.524, 116.506
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 / FXI / Plasma thromboplastin antecedent / PTA


Mass: 29741.740 Da / Num. of mol.: 2
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 Double Bridged Peptide F19


Mass: 1252.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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

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: 2.91→44 Å / Num. obs: 9337 / % possible obs: 99.9 % / Redundancy: 10.65 % / Biso Wilson estimate: 44.012 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.175 / Χ2: 1.131 / Net I/σ(I): 13.33
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
2.91-3.089.3510.7732.6513699147514650.9390.81899.3
3.08-3.2911.1020.4914.7915387138613860.9710.515100
3.29-3.5610.9620.2877.9114305130513050.9890.301100
3.56-3.8910.2450.18911.9112274119811980.9910.199100
3.89-4.3510.8530.12717.211862109310930.9960.134100
4.35-5.0111.6930.10222.36113779739730.9970.107100
5.01-6.1211.3720.1121.4295418398390.9960.115100
6.12-8.5710.9820.09225.3372486606600.9970.096100
8.57-448.9710.0633.6737504214180.9980.06499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ty6


Resolution: 2.91→43.999 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.91
RfactorNum. reflection% reflection
Rfree0.2409 428 4.59 %
Rwork0.1789 --
obs0.1816 9318 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.37 Å2 / Biso mean: 56.0434 Å2 / Biso min: 24.56 Å2
Refinement stepCycle: final / Resolution: 2.91→43.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 96 10 2049
Biso mean--54.13 43.03 -
Num. residues----246
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9063-3.32680.31171570.2491288199
3.3268-4.19090.25981380.17262924100
4.1909-43.90.19381330.1583085100
Refinement TLS params.Method: refined / Origin x: 33.4095 Å / Origin y: -20.5821 Å / Origin z: -13.6334 Å
111213212223313233
T0.3648 Å20.0439 Å20.0329 Å2-0.3195 Å2-0.0626 Å2--0.2109 Å2
L3.2492 °21.145 °21.338 °2-3.4247 °2-0.4671 °2--5.2032 °2
S-0.0051 Å °0.0255 Å °0.0566 Å °0.0052 Å °0.0084 Å °-0.0235 Å °-0.191 Å °0.1864 Å °-0.0084 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 245
2X-RAY DIFFRACTION1allH361 - 368
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allF2 - 13

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