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- PDB-8os5: Crystal structure of the Factor XII heavy chain reveals an interl... -

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Basic information

Entry
Database: PDB / ID: 8os5
TitleCrystal structure of the Factor XII heavy chain reveals an interlocking dimer with a FnII to kringle domain interaction
ComponentsCoagulation factor XII-Mie
KeywordsBLOOD CLOTTING / Factor XII heavy chain Crystal structure Thrombosis kringle domain
Function / homology
Function and homology information


coagulation factor XIIa / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Coagulation factor XII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLi, C. / Saleem, M. / Kaira, B.G. / Brown, A. / Wilson, C. / Philippou, H. / Emsley, J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
British Heart FoundationPG/16/6/31941 United Kingdom
British Heart FoundationRG/12/9/29775 United Kingdom
British Heart FoundationFS/18/70/33893 United Kingdom
CitationJournal: Blood / Year: 2020
Title: Factor XII and kininogen asymmetric assembly with gC1qR/C1QBP/P32 is governed by allostery.
Authors: Kaira, B.G. / Slater, A. / McCrae, K.R. / Dreveny, I. / Sumya, U. / Mutch, N.J. / Searle, M. / Emsley, J.
History
DepositionApr 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XII-Mie
B: Coagulation factor XII-Mie
C: Coagulation factor XII-Mie


Theoretical massNumber of molelcules
Total (without water)100,5033
Polymers100,5033
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area46200 Å2
Unit cell
Length a, b, c (Å)144.536, 144.594, 155.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Coagulation factor XII-Mie


Mass: 33501.043 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila malayana (fry) / References: UniProt: Q8IZZ5

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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: 4.05 Å3/Da / Density % sol: 69.65 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 5% PAA1200, 0.1M urea.

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.394→77.97 Å / Num. obs: 14002 / % possible obs: 94.2 % / Redundancy: 6.4 % / CC1/2: 0.994 / Net I/σ(I): 7.1
Reflection shellResolution: 3.394→3.716 Å / Num. unique obs: 701 / CC1/2: 0.585

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→77.97 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 43.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3188 1414 10.1 %
Rwork0.2548 --
obs0.2616 13995 61.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→77.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 0 0 5690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135897
X-RAY DIFFRACTIONf_angle_d1.5358005
X-RAY DIFFRACTIONf_dihedral_angle_d6.397799
X-RAY DIFFRACTIONf_chiral_restr0.083796
X-RAY DIFFRACTIONf_plane_restr0.0151073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.520.4583120.36397X-RAY DIFFRACTION5
3.52-3.660.3514330.3677322X-RAY DIFFRACTION16
3.66-3.830.4038620.3396664X-RAY DIFFRACTION33
3.83-4.030.38411140.3022917X-RAY DIFFRACTION46
4.03-4.280.37051190.29021183X-RAY DIFFRACTION57
4.28-4.610.31311670.25221455X-RAY DIFFRACTION71
4.61-5.080.26771920.22641713X-RAY DIFFRACTION84
5.08-5.810.28742200.23382001X-RAY DIFFRACTION97
5.81-7.320.30912430.28862083X-RAY DIFFRACTION100
7.32-77.970.33322520.23692146X-RAY DIFFRACTION99

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