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- PDB-3sqh: Crystal structure of prethrombin-2 mutant S195A in the the open form -

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Basic information

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


cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / 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 / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / positive regulation of protein phosphorylation / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of cell growth / : / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / 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. ...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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 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
E: Thrombin light chain, heavy chain


Theoretical massNumber of molelcules
Total (without water)33,3931
Polymers33,3931
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.359, 60.043, 49.691
Angle α, β, γ (deg.)90.00, 96.47, 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, human cDNA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00734, thrombin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 11% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 8.5

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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 20, 2011
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 13364 / Num. obs: 13204 / % possible obs: 98.8 % / Observed criterion σ(F): -0.8 / Observed criterion σ(I): -0.8 / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.2-2.243.70.323.5662197.9
2.24-2.283.60.3293.7633197.2
2.28-2.323.80.2774651198
2.32-2.373.80.2834.1664198.8
2.37-2.423.90.2594.7646197.7
2.42-2.4840.2235.5652198.8

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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: 2.2→30.17 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 16.215 / SU ML: 0.186 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -0.8 / σ(I): -0.8 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24382 661 5 %RANDOM
Rwork0.18907 ---
obs0.19185 12443 98.64 %-
all-12614 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.917 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.07 Å2
2---0.09 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 0 82 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222365
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9563195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10123.186113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.83315422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6811521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211795
X-RAY DIFFRACTIONr_mcbond_it0.5881.51411
X-RAY DIFFRACTIONr_mcangle_it1.07822274
X-RAY DIFFRACTIONr_scbond_it1.6993954
X-RAY DIFFRACTIONr_scangle_it2.6014.5921
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 50 -
Rwork0.219 894 -
obs-894 97.52 %
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)
13.1876-0.746-2.68521.3495-0.8454.43440.19430.1276-0.0723-0.1889-0.11030.09190.06160.0325-0.08410.19170.0155-0.05310.2295-0.03250.1828-23.7694.40136.8409
21.5445-0.67831.47451.7404-0.49293.0740.24530.2661-0.4367-0.3056-0.13580.00460.47270.201-0.10940.18420.03280.01580.1611-0.06230.2173-2.2375-7.04810.43
31.01361.43631.1066.74324.01632.74410.14230.4974-0.6527-0.47450.0883-0.02390.10310.0795-0.23070.56630.1044-0.11870.5103-0.35650.6648-7.5049-11.1483-1.243
45.20490.3238-0.9376.108-2.81432.9870.0445-0.2081-0.03250.3510.0182-0.11140.06820.0264-0.06270.08050.0177-0.01130.0657-0.00330.10543.25820.287221.4337
52.8668-0.0133-0.52392.78780.74032.58480.07040.1023-0.1158-0.2058-0.06340.0958-0.00490.0395-0.0070.1020.0385-0.04120.12390.02350.0911-10.9124.51019.6007
68.28950.0296-5.10340.0946-0.00513.1481-0.8631-1.0603-1.32450.32470.0107-0.01090.56280.69050.85241.28570.1045-0.11410.747-0.08051.4929-15.5472-17.601918.5832
73.2424-0.1996-0.27631.7275-0.00523.74080.1409-0.6212-0.12070.5114-0.02930.17770.2532-0.3052-0.11170.2163-0.04020.03920.1920.01660.1665-15.4361.697626.2535
83.73172.0188-2.27881.1112-1.20691.4545-0.3211-0.1226-0.4499-0.0613-0.0801-0.20210.3604-0.0740.40130.8203-0.23960.11090.7036-0.05490.7026-26.2394-4.835624.3078
94.7685-1.74941.67483.27920.33673.81750.0021-0.3244-0.25070.23650.10520.29650.2927-0.3299-0.10720.0768-0.0010.03360.1177-0.02270.0829-13.69292.880918.2035
104.71551.2414-3.0943.8638-0.492912.64330.13670.59870.2474-0.3574-0.1312-0.0951-0.4686-0.1254-0.00550.13770.03280.01570.13060.04650.23354.846510.587411.7019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 24
2X-RAY DIFFRACTION2E25 - 72
3X-RAY DIFFRACTION3E73 - 85
4X-RAY DIFFRACTION4E86 - 106
5X-RAY DIFFRACTION5E107 - 145
6X-RAY DIFFRACTION6E146 - 153
7X-RAY DIFFRACTION7E154 - 184
8X-RAY DIFFRACTION8E185 - 191
9X-RAY DIFFRACTION9E192 - 234
10X-RAY DIFFRACTION10E235 - 247

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