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- PDB-3hk6: Crystal structure of murine thrombin mutant W215A/E217A (two mole... -

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Basic information

Entry
Database: PDB / ID: 3hk6
TitleCrystal structure of murine thrombin mutant W215A/E217A (two molecules in the asymmetric unit)
Components
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE / Serine protease / Acute phase / Blood coagulation / Calcium / Cleavage on pair of basic residues / Disulfide bond / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Protease / Zymogen
Function / homology
Function and homology information


Common Pathway of Fibrin Clot Formation / Platelet Aggregation (Plug Formation) / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Intrinsic Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / thrombin-activated receptor signaling pathway / Peptide ligand-binding receptors / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade ...Common Pathway of Fibrin Clot Formation / Platelet Aggregation (Plug Formation) / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Intrinsic Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / thrombin-activated receptor signaling pathway / Peptide ligand-binding receptors / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade / G alpha (q) signalling events / Cell surface interactions at the vascular wall / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / thrombin / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / fibrinolysis / regulation of cytosolic calcium ion concentration / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / negative regulation of proteolysis / lipopolysaccharide binding / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / positive regulation of reactive oxygen species metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / peptidase activity / heparin binding / regulation of cell shape / regulation of gene expression / positive regulation of cell growth / collagen-containing extracellular matrix / endopeptidase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space
Similarity search - Function
Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site ...Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Few Secondary Structures / Irregular / 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGandhi, P.S. / Page, M.J. / Chen, Z. / Bush-Pelc, L. / Di Cera, E.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A.
Authors: Gandhi, P.S. / Page, M.J. / Chen, Z. / Bush-Pelc, L. / Di Cera, E.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket.
Authors: Pineda, A.O. / Chen, Z.W. / Caccia, S. / Cantwell, A.M. / Savvides, S.N. / Waksman, G. / Mathews, F.S. / Di Cera, E.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin light chain
B: Thrombin heavy chain
C: Thrombin light chain
D: Thrombin heavy chain


Theoretical massNumber of molelcules
Total (without water)69,8024
Polymers69,8024
Non-polymers00
Water00
1
A: Thrombin light chain
B: Thrombin heavy chain


Theoretical massNumber of molelcules
Total (without water)34,9012
Polymers34,9012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-15.2 kcal/mol
Surface area13980 Å2
MethodPISA
2
C: Thrombin light chain
D: Thrombin heavy chain


Theoretical massNumber of molelcules
Total (without water)34,9012
Polymers34,9012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-17.2 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.394, 70.394, 293.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE BIOLOGICAL ASSEMBLY CONSISTS OF A AND B CHAINS.

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Components

#1: Protein/peptide Thrombin light chain / Coagulation factor II


Mass: 5105.731 Da / Num. of mol.: 2 / Fragment: Light chain: UNP residues 317-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: F2, Cf2 / Cell (production host): BHK cells / Organ (production host): baby hamster kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19221, thrombin
#2: Protein Thrombin heavy chain / Coagulation factor II


Mass: 29795.461 Da / Num. of mol.: 2 / Fragment: Heavy chain: UNP residues 361-618 / Mutation: W215A, E217A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: F2, Cf2 / Cell (production host): BHK cells / Organ (production host): baby hamster kidney / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19221, thrombin
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 200mM Ammonium dihydrogen phosphate, 14% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: MACSCIENCE / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 14, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 13077 / Num. obs: 12201 / % possible obs: 93.3 % / Observed criterion σ(I): -1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.6
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.5 / Num. unique all: 437 / % possible all: 72.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TQ0

1tq0


Resolution: 3.2→40 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.803 / SU B: 27.591 / SU ML: 0.489 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.679 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31419 583 4.8 %RANDOM
Rwork0.22177 ---
obs0.22616 11572 93.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.848 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å20 Å2
2--2.19 Å20 Å2
3----4.37 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4882 0 0 0 4882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225010
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9526776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2035596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66923.077234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.28715884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5151542
X-RAY DIFFRACTIONr_chiral_restr0.1280.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213796
X-RAY DIFFRACTIONr_mcbond_it0.681.52992
X-RAY DIFFRACTIONr_mcangle_it1.30424840
X-RAY DIFFRACTIONr_scbond_it1.7232018
X-RAY DIFFRACTIONr_scangle_it2.9814.51936
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 31 -
Rwork0.235 630 -
obs--73.04 %

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