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- PDB-2afq: 1.9 angstrom crystal structure of wild-type human thrombin in the... -

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Basic information

Entry
Database: PDB / ID: 2afq
Title1.9 angstrom crystal structure of wild-type human thrombin in the sodium free state
Components(Prothrombin) x 2
KeywordsBLOOD CLOTTING / HYDROLASE / alpha-thrombin / coagulation / allostery / protease / coagulation factor II
Function / homology
Function and homology information


cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway ...cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / 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 / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / growth factor activity / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / response to wounding / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of protein phosphorylation / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsJohnson, D.J.D. / Adams, T.E. / Huntington, J.A.
CitationJournal: Biochem.J. / Year: 2005
Title: Crystal structure of wild-type human thrombin in the Na+-free state
Authors: Johnson, D.J.D. / Adams, T.E. / Li, W. / Huntington, J.A.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 14, 2016Group: Structure summary
Revision 1.5Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 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: Prothrombin
B: Prothrombin
C: Prothrombin
D: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,95511
Polymers66,3104
Non-polymers6457
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-23 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.340, 82.310, 50.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-663-

HOH

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Components

#1: Protein/peptide Prothrombin / E.C.3.4.21.5 / Coagulation factor II


Mass: 3374.793 Da / Num. of mol.: 2 / Fragment: Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: pET23(+)-pre2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00734, thrombin
#2: Protein Prothrombin / E.C.3.4.21.5 / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 2 / Fragment: Heavy Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: pET23(+)-pre2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00734, thrombin
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.29 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3350, magnesium acetate, lithium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2005 / Details: Rh coated Si mirror
RadiationMonochromator: triangular single crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.93→50.9 Å / Num. all: 49378 / Num. obs: 49378 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.103 / Net I/σ(I): 14.6
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.1 / Num. unique all: 7065 / Rsym value: 0.55 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
ARP/wARPmodel building
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PPB

1ppb


Resolution: 1.93→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2052606.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1513 3.1 %RANDOM
Rwork0.197 ---
all0.203 49332 --
obs0.198 49279 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.587 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å20 Å2
2---2.62 Å20 Å2
3----0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.93→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 42 478 4846
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.032.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 250 3.1 %
Rwork0.259 7805 -
all-8055 -
obs-7805 99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2water_rep.topwater_rep.param
X-RAY DIFFRACTION3gol.topgol.par

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