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- PDB-5i25: human recombinant coagulation FXI in complex with a peptide deriv... -

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Basic information

Entry
Database: PDB / ID: 5i25
Titlehuman recombinant coagulation FXI in complex with a peptide derived from human high molecular weight kininogen (HKP)
Components
  • ASN-PRO-ILE-SER-ASP-PHE-PRO-ASP
  • Coagulation factor XIFactor XI
KeywordsHYDROLASE / Coagulation FXI / high molecular weight kininogen
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / negative regulation of cell adhesion / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / negative regulation of cell adhesion / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / negative regulation of proteolysis / Post-translational protein phosphorylation / hormone activity / vasodilation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / heparin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Cystatin domain / Cystatin-like domain / Cystatin domain ...HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Cystatin domain / Cystatin-like domain / Cystatin domain / Apple domain. / Apple domain / APPLE domain / Cystatin superfamily / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 3-Layer(bba) Sandwich / 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 / Alpha Beta
Similarity search - Domain/homology
Kininogen-1 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å
AuthorsHall, G.A.F. / Wong, S.S. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart Foundation United Kingdom
CitationJournal: Blood / Year: 2016
Title: A novel DFP tripeptide motif interacts with the coagulation factor XI apple 2 domain.
Authors: Wong, S.S. / stergaard, S. / Hall, G. / Li, C. / Williams, P.M. / Stennicke, H. / Emsley, J.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XI
B: ASN-PRO-ILE-SER-ASP-PHE-PRO-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6845
Polymers69,0212
Non-polymers6643
Water95553
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-1 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.590, 80.590, 251.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Coagulation factor XI / Factor XI / FXI / Plasma thromboplastin antecedent / PTA


Mass: 68116.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03951, coagulation factor XIa
#2: Protein/peptide ASN-PRO-ILE-SER-ASP-PHE-PRO-ASP


Mass: 903.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: P01042*PLUS
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.01 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.4 / Details: PEG1500, HEPES pH 7.4., 0.2M NaCl

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.85→39.79 Å / Num. obs: 20319 / % possible obs: 99 % / Redundancy: 6 % / Rmerge(I) obs: 0.083 / Net I/av σ(I): 3 / Net I/σ(I): 16
Reflection shellHighest resolution: 2.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 16 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.85→39.79 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28821 2057 10.2 %RANDOM
Rwork0.22639 ---
obs0.23249 18148 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 74.251 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.85→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 42 53 4842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.956668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0115600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25923.726212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.00415830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1061527
X-RAY DIFFRACTIONr_chiral_restr0.1020.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213661
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2341.53002
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.29124873
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.48731914
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.4264.51795
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 148 -
Rwork0.329 1298 -
obs--99.93 %

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