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- PDB-4fub: Crystal Structure of the Urokinase -

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Basic information

Entry
Database: PDB / ID: 4fub
TitleCrystal Structure of the Urokinase
ComponentsUrokinase-type plasminogen activatorUrokinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / tertiary granule membrane / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / specific granule membrane / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. ...Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / 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
Chem-4UP / ACETATE ION / SUCCINIC ACID / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKang, Y.N. / Stuckey, J.A. / Nienaber, V. / Giranda, V.
CitationJournal: to be published
Title: Crystal Structure of the Urokinase
Authors: Kang, Y.N. / Stuckey, J.A. / Nienaber, V. / Giranda, V.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,59616
Polymers27,7161
Non-polymers2,88015
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.100, 52.400, 80.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Urokinase-type plasminogen activator / Urokinase / U-plasminogen activator / uPA / Urokinase-type plasminogen activator long chain A / Urokinase-type ...U-plasminogen activator / uPA / Urokinase-type plasminogen activator long chain A / Urokinase-type plasminogen activator short chain A / Urokinase-type plasminogen activator chain B


Mass: 27715.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Escherichia coli (E. coli) / References: UniProt: P00749, u-plasminogen activator

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Non-polymers , 7 types, 259 molecules

#2: Chemical ChemComp-4UP / 6-[(2S,3S)-3-phenyloxiran-2-yl]naphthalene-2-carboximidamide


Mass: 288.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N2O
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#7: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.15 M Li2SO4, 20% polyethylene glycol MW 4000 in succinate buffer, pH 4.8-6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
PH range: 4.8-6.0

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / % possible obs: 86.3 % / Rmerge(I) obs: 0.122 / Χ2: 1.259 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.640.6619090.548144.5
1.64-1.680.6915320.567173.5
1.68-1.720.65717130.564183.5
1.72-1.770.57917600.62185.6
1.77-1.830.48417510.635185.4
1.83-1.90.41717570.722185.1
1.9-1.970.32717830.898185.4
1.97-2.060.26417901.087186.7
2.06-2.170.20818741.297189.6
2.17-2.310.1819291.386192.6
2.31-2.490.14419991.564195.7
2.49-2.740.12720351.612197
2.74-3.130.10420611.718197.2
3.13-3.940.07721071.714197.6
3.94-400.08220941.927192.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→17.74 Å / Cor.coef. Fo:Fc: 0.9521 / Cor.coef. Fo:Fc free: 0.9409 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 885 5.04 %RANDOM
Rwork0.1551 ---
obs0.1567 17554 93.02 %-
Displacement parametersBiso max: 70.11 Å2 / Biso mean: 18.5997 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.0145 Å20 Å20 Å2
2--3.6465 Å20 Å2
3----1.632 Å2
Refine analyzeLuzzati coordinate error obs: 0.164 Å
Refinement stepCycle: LAST / Resolution: 1.9→17.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 100 244 2246
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d936SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes324HARMONIC5
X-RAY DIFFRACTIONt_it2076HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion267SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2496SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2076HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2811HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.97
X-RAY DIFFRACTIONt_other_torsion2.63
LS refinement shellResolution: 1.9→2.02 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2329 123 4.8 %
Rwork0.1601 2438 -
all0.1636 2561 -
obs--93.02 %
Refinement TLS params.Method: refined / Origin x: -13.7272 Å / Origin y: -9.4447 Å / Origin z: 10.9941 Å
111213212223313233
T-0.0417 Å20.0006 Å2-0.0008 Å2--0.044 Å20.0054 Å2---0.0214 Å2
L0.5105 °2-0.0182 °20.0263 °2-0.8233 °20.1096 °2--0.561 °2
S-0.0004 Å °-0.0224 Å °-0.0102 Å °0.0069 Å °0.0055 Å °-0.0156 Å °-0.0007 Å °0.0061 Å °-0.0051 Å °
Refinement TLS groupSelection details: { A|1 - A|246 }

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