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- PDB-4bdx: The structure of the FnI-EGF tandem domain of coagulation factor XII -

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Basic information

Entry
Database: PDB / ID: 4bdx
TitleThe structure of the FnI-EGF tandem domain of coagulation factor XII
ComponentsCOAGULATION FACTOR XIIA HEAVY CHAINFactor XII
KeywordsHYDROLASE / FNI DOMAIN / EGF 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 / Laminin / Laminin / 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 / Ribbon / 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 / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Coagulation factor XII
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.62 Å
AuthorsBeringer, D.X. / Kroon-Batenburg, L.M.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The Structure of the Fni-Egf-Like Tandem Domain of Coagulation Factor Xii Solved Using Siras.
Authors: Beringer, D.X. / Kroon-Batenburg, L.M.J.
History
DepositionOct 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Other / Structure summary
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COAGULATION FACTOR XIIA HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5982
Polymers9,5391
Non-polymers591
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.788, 96.788, 47.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2027-

HOH

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Components

#1: Protein COAGULATION FACTOR XIIA HEAVY CHAIN / Factor XII / COAGULATION FACTOR XII / HAGEMAN FACTOR / HAF


Mass: 9538.882 Da / Num. of mol.: 1 / Fragment: FNI-EGF, RESIDUES 133-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZALPHA / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: P00748, coagulation factor XIIa
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.93 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS PH 8.5 16-18% PEG4, 0.2 M POTASSIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.03961
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2010 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03961 Å / Relative weight: 1
ReflectionResolution: 1.62→48.39 Å / Num. obs: 14626 / % possible obs: 99.7 % / Observed criterion σ(I): 3.5 / Redundancy: 23.5 % / Biso Wilson estimate: 21.03 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.6
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.5 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.62→48.394 Å / SU ML: 0.18 / σ(F): 1.53 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 1389 5.1 %
Rwork0.2156 --
obs0.2171 14618 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→48.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 0 4 67 724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008709
X-RAY DIFFRACTIONf_angle_d1.128953
X-RAY DIFFRACTIONf_dihedral_angle_d14.871264
X-RAY DIFFRACTIONf_chiral_restr0.08195
X-RAY DIFFRACTIONf_plane_restr0.005131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6201-1.6780.25921610.27782506X-RAY DIFFRACTION97
1.678-1.74510.25171630.25252585X-RAY DIFFRACTION100
1.7451-1.82460.22771500.21772607X-RAY DIFFRACTION100
1.8246-1.92080.21421450.20592566X-RAY DIFFRACTION100
1.9208-2.04110.23431500.21862597X-RAY DIFFRACTION100
2.0411-2.19870.22641330.20192631X-RAY DIFFRACTION100
2.1987-2.420.22961090.21772625X-RAY DIFFRACTION100
2.42-2.77010.24231270.23362622X-RAY DIFFRACTION100
2.7701-3.48990.25731230.21442599X-RAY DIFFRACTION100
3.4899-48.41560.26651280.20482638X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.9083-0.6294-2.63545.163-1.30138.0043-0.1330.1809-0.2477-0.33090.06640.23560.2191-0.18880.01460.0688-0.0247-0.0030.09640.00410.1868.3010.5375-27.8942
26.0320.32536.78255.93641.18087.7451-0.1949-1.026-0.50610.55740.0986-0.85450.74260.93940.06660.24660.12670.02090.61460.09350.335418.9673-1.0174-20.7072
36.64652.83845.94443.03181.81146.27890.03630.1331-1.06510.01280.1777-0.51020.61670.758-0.26980.16370.05560.07360.3644-0.02410.364917.9645-4.2491-28.2093
45.1613-0.9658-2.5786.42623.78757.78740.0418-0.18120.3783-0.5429-0.3432-0.4836-0.88250.56970.22920.2919-0.0123-0.05890.91340.10540.258724.38926.7199-13.545
52.31720.581.12680.64830.16380.57490.0075-0.93390.62860.2117-0.69420.6374-0.2765-0.89270.5450.33650.0417-0.13891.4044-0.34060.468111.19237.0125-9.4499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:18 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 19:27 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 28:43 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 44:69 )
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 70:84 )

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