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- PDB-6b77: Structures of the two-chain human plasma factor XIIa co-crystalli... -

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Basic information

Entry
Database: PDB / ID: 6b77
TitleStructures of the two-chain human plasma factor XIIa co-crystallized with potent inhibitors
Components(Coagulation factor ...Coagulation) x 2
KeywordsBLOOD CLOTTING / Structural characterization of human plasma Factor XIIa in complexes with inhibitors
Function / homology
Function and homology information


coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / positive regulation of fibrinolysis / misfolded protein binding / zymogen activation ...coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / positive regulation of fibrinolysis / misfolded protein binding / zymogen activation / Defective factor XII causes hereditary angioedema / protein autoprocessing / rough endoplasmic reticulum / positive regulation of blood coagulation / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / protein processing / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Coagulation factor XII/hepatocyte growth factor activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Coagulation factor XII/hepatocyte growth factor activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like 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
[3-(1-aminoisoquinolin-6-yl)phenyl]boronic acid / IODIDE ION / Coagulation factor XII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsDementiev, A.A. / Silva, A. / Yee, C. / Flavin, M.T. / Partridge, J.R.
CitationJournal: Blood Adv / Year: 2018
Title: Structures of human plasma beta-factor XIIa cocrystallized with potent inhibitors.
Authors: Dementiev, A. / Silva, A. / Yee, C. / Li, Z. / Flavin, M.T. / Sham, H. / Partridge, J.R.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 XII
B: Coagulation factor XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,38210
Polymers27,0592
Non-polymers1,3238
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.402, 79.402, 122.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Coagulation factor ... , 2 types, 2 molecules AB

#1: Protein/peptide Coagulation factor XII / Factor XII / Hageman factor / HAF


Mass: 932.037 Da / Num. of mol.: 1 / Fragment: UNP residues 354-362 / Source method: isolated from a natural source / Details: Activated Factor XIIa Part 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P00748, coagulation factor XIIa
#2: Protein Coagulation factor XII / Factor XII / Hageman factor / HAF


Mass: 26127.395 Da / Num. of mol.: 1 / Fragment: UNP residues 373-615 / Source method: isolated from a natural source / Details: Activated Factor XIIa Light Chain / Source: (natural) Homo sapiens (human) / References: UniProt: P00748, coagulation factor XIIa

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-4-deoxy-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 104 molecules

#4: Chemical ChemComp-CWV / [3-(1-aminoisoquinolin-6-yl)phenyl]boronic acid


Mass: 264.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13BN2O2
#5: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30 mM HEPES, 0.2 M NH4I, 0.2 M NH4S04

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 15282 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.4
Reflection shellResolution: 2.37→2.47 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1524 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MJG

3mjg


Resolution: 2.37→41.35 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2176 1525 9.98 %
Rwork0.1736 --
obs-15275 99.7 %
Refinement stepCycle: LAST / Resolution: 2.37→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 70 97 2015
LS refinement shellResolution: 2.37→2.45 Å
RfactorNum. reflection% reflection
Rfree0.32 137 10 %
Rwork0.24 1219 -
obs--97 %

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