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

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Basic information

Entry
Database: PDB / ID: 7prk
TitleFactor XII Fibronectin type II (FXII FnII) domain
ComponentsCoagulation factor 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 / positive regulation of blood coagulation / rough endoplasmic reticulum / 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
FORMIC ACID / Coagulation factor XII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 1.1May 1, 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)8,5733
Polymers8,4621
Non-polymers1112
Water75742
1
A: Coagulation factor XII
hetero molecules

A: Coagulation factor XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1466
Polymers16,9232
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1300 Å2
ΔGint-83 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.820, 45.820, 53.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-101-

ZN

21A-238-

HOH

31A-241-

HOH

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Components

#1: Protein Coagulation 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.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.66 Å3/Da / Density % sol: 25.87 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / Details: 0.1 M Sodium Cacodylate, 25 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2821 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2821 Å / Relative weight: 1
ReflectionResolution: 1.64→34.8 Å / Num. obs: 7469 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Net I/σ(I): 26.6
Reflection shellResolution: 1.64→1.67 Å / Num. unique obs: 351 / CC1/2: 0.983

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FXII FnII from unpublished structure

Resolution: 1.64→34.8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.624 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 398 5.4 %RANDOM
Rwork0.1696 ---
obs0.1713 7036 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.7 Å2 / Biso mean: 22.474 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.05 Å2
Refinement stepCycle: final / Resolution: 1.64→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms450 0 4 42 496
Biso mean--23.33 31.9 -
Num. residues----54
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019471
X-RAY DIFFRACTIONr_bond_other_d0.0060.02405
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.897642
X-RAY DIFFRACTIONr_angle_other_deg0.9813933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.197553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.86522.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.351564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.113153
X-RAY DIFFRACTIONr_chiral_restr0.0960.262
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02127
LS refinement shellResolution: 1.64→1.681 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.204 28 -
Rwork0.175 502 -
obs--99.81 %

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