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- PDB-3nxp: Crystal structure of human prethrombin-1 -

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Basic information

Entry
Database: PDB / ID: 3nxp
TitleCrystal structure of human prethrombin-1
ComponentsPrethrombin-1
KeywordsHYDROLASE / Thrombin / prethrombin-1 / allostery / blood coagulation / kringle / serine protease / zymogen
Function / homology
Function and homology information


positive regulation of lipid kinase activity / 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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / 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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / 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 / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / 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 / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Plasminogen Kringle 4 / Plasminogen Kringle 4 / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / 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 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: 2.2 Å
AuthorsChen, Z. / Bush-Pelc, L.A. / Di Cera, E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of prethrombin-1.
Authors: Chen, Z. / Pelc, L.A. / Di Cera, E.
#1: Journal: CELL.MOL.LIFE SCI. / Year: 2008
Title: NA(+) binding to meizothrombin DESF1.
Authors: Papaconstantinou, M.E. / Gandhi, P.S. / Chen, Z. / Bah, A. / Di Cera, E.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prethrombin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4866
Polymers47,8371
Non-polymers6505
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.893, 81.006, 88.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Prethrombin-1 / Coagulation factor II


Mass: 47836.688 Da / Num. of mol.: 1 / Fragment: UNP residues 199-622 / Mutation: R271A, R284A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): BHK / References: UniProt: P00734, thrombin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl, pH 8.5 and 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2010
RadiationMonochromator: NE-CAT, 24-ID-E / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 25400 / Num. obs: 24257 / % possible obs: 95.5 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2351 / % possible all: 94.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPfrom ccp4phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E6P

3e6p


Resolution: 2.2→59.74 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU ML: 0.138 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -0.5 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1244 5.1 %RANDOM
Rwork0.1975 ---
obs0.19895 22995 95.5 %-
all-24078 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å20 Å2
2---2.75 Å2-0 Å2
3---2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 42 197 3351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223236
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.964378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79523.875160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8815540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0291524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212490
X-RAY DIFFRACTIONr_mcbond_it0.4651.51934
X-RAY DIFFRACTIONr_mcangle_it0.88723106
X-RAY DIFFRACTIONr_scbond_it1.59431302
X-RAY DIFFRACTIONr_scangle_it2.4984.51272
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 83 -
Rwork0.272 1643 -
obs-1643 92.95 %
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)
19.2247-0.5155-0.17381.43180.59023.10070.0151-0.69320.05510.65290.1243-0.13350.15780.0948-0.13940.3150.0132-0.04660.2109-0.02030.05568.491-14.53931.883
22.15350.4599-0.27762.7152-0.0611.69220.0231-0.0574-0.1386-0.09-0.00260.37250.2238-0.232-0.02050.09760.01930.00090.14840.00280.107-10.139-18.84417.621
31.8744-0.3383-0.61881.21340.15691.3360.08620.00640.1803-0.02750.00210.0036-0.1538-0.0039-0.08830.0948-0.0198-0.00720.0872-0.01730.07645.083-7.96315.551
41.1355-0.54350.15623.4951-0.45490.43690.00630.0776-0.1664-0.2338-0.02160.23370.139-0.06010.01530.0789-0.00830.0010.0926-0.00310.0614-2.352-24.37814.175
53.0826-0.3316-1.44993.0260.51842.66070.05940.3037-0.0253-0.2956-0.0306-0.2633-0.18580.1139-0.02880.1371-0.0134-0.07290.1716-0.01150.1221-0.784-21.4563.266
65.8357-0.51882.8530.5211-0.92312.66470.0890.3586-0.2282-0.06590.0333-0.09580.13530.1207-0.12220.13510.0063-0.01080.1263-0.04360.1329-2.505-26.6362.093
72.23020.12610.28761.1861-0.06980.74270.0091-0.02-0.01910.03340.0249-0.0312-0.02760.1624-0.0340.08770.00750.00510.0746-0.00950.08235.605-20.21815.059
812.39333.58138.20195.8139-1.314417.7197-0.1901-0.339-1.4063-0.10820.237-0.2251.2320.2084-0.04690.30.10960.08160.16210.07170.361624.156-34.0715.165
94.9697-0.88130.97093.0484-0.55643.37620.1049-0.243-0.11350.0041-0.0707-0.46120.05170.5426-0.03420.06060.02120.01430.2624-0.00350.15732.433-21.08814.173
100.0161-0.01130.00590.03120.03360.0652-0.00590.07480.17180.1993-0.1476-0.05580.3406-0.0970.15352.1838-0.17860.0841.55110.08842.263930.614-16.09329.455
112.3065-0.89951.498814.06442.92761.88570.1527-0.5989-0.7760.59580.35480.2910.3027-0.2741-0.50750.21170.1725-0.05470.73990.20240.308334.152-26.48922.101
124.571.3618-0.37823.30530.29023.30220.0023-0.16530.0108-0.01760.01690.12690.05890.3459-0.01920.0820.0246-0.01930.18410.01660.080224.735-21.77417.179
1381.574716.178544.87773.312710.496163.56710.27452.8187-4.76410.04420.6888-0.9948-0.422-2.1573-0.96340.67320.0510.32961.3016-0.84841.2258.177-37.47611.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 3
2X-RAY DIFFRACTION2A4 - 37
3X-RAY DIFFRACTION3A38 - 126
4X-RAY DIFFRACTION4A127 - 145
5X-RAY DIFFRACTION5A146 - 175
6X-RAY DIFFRACTION6A176 - 192
7X-RAY DIFFRACTION7A193 - 247
8X-RAY DIFFRACTION8F7 - 15
9X-RAY DIFFRACTION9F16 - 33
10X-RAY DIFFRACTION10F34 - 46
11X-RAY DIFFRACTION11F47 - 57
12X-RAY DIFFRACTION12F58 - 87
13X-RAY DIFFRACTION13F88 - 95

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