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- PDB-3hk3: Crystal structure of murine thrombin mutant W215A/E217A (one mole... -

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Basic information

Entry
Database: PDB / ID: 3hk3
TitleCrystal structure of murine thrombin mutant W215A/E217A (one molecule 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 / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of reactive oxygen species metabolic process / peptidase activity / heparin binding / regulation of cell shape / positive regulation of cell growth / regulation of gene expression / 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
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. ...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 / 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
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 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

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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


Theoretical massNumber of molelcules
Total (without water)34,9012
Polymers34,9012
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-7.3 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.647, 63.939, 95.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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.: 1 / 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.: 1 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 200mM Ammonium chloride, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 7, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.94→43.31 Å / Num. all: 22440 / Num. obs: 21296 / % possible obs: 94.9 % / Observed criterion σ(I): -1 / Redundancy: 5.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.2
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.3 / Num. unique all: 949 / % possible all: 87

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TQ0

1tq0


Resolution: 1.94→43.31 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.456 / SU ML: 0.101 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.183 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23545 1098 5.2 %RANDOM
Rwork0.18075 ---
obs0.1834 20160 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.94→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 240 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222348
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9573174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79222.87108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70415419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3581521
X-RAY DIFFRACTIONr_chiral_restr0.0960.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211770
X-RAY DIFFRACTIONr_mcbond_it0.7271.51402
X-RAY DIFFRACTIONr_mcangle_it1.38722267
X-RAY DIFFRACTIONr_scbond_it2.1933946
X-RAY DIFFRACTIONr_scangle_it3.5774.5907
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 61 -
Rwork0.212 1314 -
obs--85.88 %

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