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- PDB-3sqe: Crystal structure of prethrombin-2 mutant S195A in the alternativ... -

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Basic information

Entry
Database: PDB / ID: 3sqe
TitleCrystal structure of prethrombin-2 mutant S195A in the alternative form
ComponentsThrombin light chain, heavy chain
KeywordsHYDROLASE / Serine protease / Prethrombin-2
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / 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 / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPozzi, N. / Chen, Z. / Di Cera, E.
Citation
Journal: Biochemistry / Year: 2011
Title: Crystal structures of prethrombin-2 reveal alternative conformations under identical solution conditions and the mechanism of zymogen activation.
Authors: Pozzi, N. / Chen, Z. / Zapata, F. / Pelc, L.A. / Barranco-Medina, S. / Di Cera, E.
#1: Journal: Protein Sci. / Year: 1994
Title: The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin.
Authors: Vijayalakshmi, J. / Padmanabhan, K.P. / Mann, K.G. / Tulinsky, A.
History
DepositionJul 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Thrombin light chain, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5773
Polymers33,3931
Non-polymers1842
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.378, 58.055, 52.880
Angle α, β, γ (deg.)90.00, 98.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thrombin light chain, heavy chain


Mass: 33393.270 Da / Num. of mol.: 1 / Fragment: unp residues 333-622 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00734, thrombin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 11% PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2011
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 21201 / Num. obs: 20289 / % possible obs: 95.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.9-1.936.30.2158.5993193.5
1.93-1.976.40.2029.6987193.3
1.97-2.016.40.18310.6988192.7
2.01-2.056.40.16212.2967194.1
2.05-2.096.50.15113.3980193.8
2.09-2.146.50.132151002194.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPfrom ccp4phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HAG

1hag


Resolution: 1.9→25.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.508 / SU ML: 0.089 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 1046 5.2 %RANDOM
Rwork0.17136 ---
obs0.17313 19193 95.61 %-
all-20074 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.937 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 12 210 2558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222439
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.963301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.235296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76223.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5151521
X-RAY DIFFRACTIONr_chiral_restr0.0960.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211863
X-RAY DIFFRACTIONr_mcbond_it0.9771.51460
X-RAY DIFFRACTIONr_mcangle_it1.84322359
X-RAY DIFFRACTIONr_scbond_it2.1853979
X-RAY DIFFRACTIONr_scangle_it3.6494.5942
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 89 -
Rwork0.184 1363 -
obs-1363 92.78 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23520.13323.25281.5972-0.01492.946-0.07580.33930.0592-0.18320.05420.0714-0.15960.21210.02160.18880.029-0.00780.18010.00570.07653.50446.8612-0.1091
23.75841.5391-2.76280.9744-0.32642.2077-0.0664-0.1203-0.0045-0.0328-0.01790.06320.05250.11690.08430.1140.0208-0.0190.17120.01270.1346-8.1614.16214.226
30.2906-0.03420.49830.55480.40080.86480.09190.0272-0.0263-0.0177-0.0269-0.0070.17740.0352-0.0650.18310.0143-0.01070.1529-0.01420.110115.573-6.33812.726
40.72930.25281.1030.53010.07121.76690.03110.1222-0.0737-0.0816-0.01190.0390.17560.215-0.01920.18060.045-0.00840.1596-0.06150.122917.3435-11.18848.6979
50.8074-0.17680.53090.0284-0.19041.82190.01140.0640.00570.0596-0.0161-0.07090.09210.01940.00470.16550.0071-0.00110.1313-0.02230.132224.871-0.21817.751
60.6521-0.23560.25440.84460.38450.5542-0.01250.04860.003-0.0057-0.01080.1007-0.0578-0.00420.02330.13310.00510.00040.1325-0.0050.1117.7734.12712.617
71.0922-0.59640.16440.97291.13411.98460.0691-0.1578-0.24190.0634-0.12970.1870.1127-0.33560.06060.1383-0.07210.03140.13030.0120.14742.832-6.0121.155
81.2226-0.34540.38840.19690.12150.5267-0.043-0.309-0.07640.05240.0310.04590.0391-0.13380.0120.1539-0.00190.00740.21780.02050.12649.37143.295221.4854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 13
2X-RAY DIFFRACTION2E14 - 17
3X-RAY DIFFRACTION3E18 - 59
4X-RAY DIFFRACTION4E60 - 83
5X-RAY DIFFRACTION5E84 - 112
6X-RAY DIFFRACTION6E113 - 147
7X-RAY DIFFRACTION7E148 - 167
8X-RAY DIFFRACTION8E168 - 246

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