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- PDB-7prj: Factor XII Fibronectin type II (FXII FnII) domain -

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Basic information

Entry
Database: PDB / ID: 7prj
TitleFactor XII Fibronectin type II (FXII FnII) domain
ComponentsCoagulation factor XIIFactor XII
KeywordsBLOOD CLOTTING / FXII Fibronectin type II (FnII) domain
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 / 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 / molecular replacement / Resolution: 1.2 Å
AuthorsKaira, B.G. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationRG/12/9/29775 United Kingdom
CitationJournal: To Be Published
Title: Factor XII Fibronectin type II (FXII FnII) domain
Authors: Kaira, B.G. / Emsley, J.
History
DepositionSep 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6584
Polymers8,4621
Non-polymers1963
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-71 kcal/mol
Surface area3840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.350, 40.880, 45.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 8461.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F12 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P00748, coagulation factor XIIa
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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

CrystalDensity Matthews: 1.44 Å3/Da
Crystal growTemperature: 292.15 K / Method: vapor diffusion
Details: 0.01 M Zinc chloride, 0.1 M Sodium acetate pH 5.0, 20 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.2821 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 7, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2821 Å / Relative weight: 1
ReflectionResolution: 1.2→30.36 Å / Num. obs: 15507 / % possible obs: 97.3 % / Redundancy: 4.5 % / CC1/2: 0.993 / Net I/σ(I): 4.02
Reflection shellResolution: 1.2→3.79 Å / Num. unique obs: 15507 / CC1/2: 0.993

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H8P

1h8p


Resolution: 1.2→22.781 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 778 5.04 %
Rwork0.1922 14671 -
obs0.1944 15449 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.78 Å2 / Biso mean: 20.8 Å2 / Biso min: 5.56 Å2
Refinement stepCycle: final / Resolution: 1.2→22.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms460 0 3 59 522
Biso mean--37.5 34.28 -
Num. residues----55
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007482
X-RAY DIFFRACTIONf_angle_d0.99657
X-RAY DIFFRACTIONf_chiral_restr0.0463
X-RAY DIFFRACTIONf_plane_restr0.00787
X-RAY DIFFRACTIONf_dihedral_angle_d13.195171
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.27520.29851110.2414237496
1.2752-1.37370.28881110.2241239496
1.3737-1.51190.25581450.2088241497
1.5119-1.73060.23021590.2018242899
1.7306-2.18010.24051360.1949245597
2.1801-3.790.21811160.1724260697

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