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- PDB-5lhs: The ligand free catalytic domain of murine urokinase-type plasmin... -

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Basic information

Entry
Database: PDB / ID: 5lhs
TitleThe ligand free catalytic domain of murine urokinase-type plasminogen activator
ComponentsUrokinase-type plasminogen activator
KeywordsHYDROLASE / Trypsin-like serine proteases / Ligand free
Function / homology
Function and homology information


Dissolution of Fibrin Clot / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / serine-type endopeptidase complex ...Dissolution of Fibrin Clot / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / serine-type endopeptidase complex / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / Neutrophil degranulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / extracellular space
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. ...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, serine 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
NICKEL (II) ION / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.047 Å
AuthorsKromann-Hansen, T. / Lange, E.L. / Sorensen, H.P. / Ghassabeh, G.H. / Huang, M. / Jensen, J.K. / Muyldermans, S. / Declerck, P.J. / Andreasen, P.A.
Funding support Denmark, China, 4items
OrganizationGrant numberCountry
Danish National Research Foundation26-331-6 Denmark
Lundbeck FoundationR83-A7826 Denmark
Carlsberg FoundationCF15-0814 Denmark
Natural Science Foundation of China31161130356, 31170707, 31370737 China
CitationJournal: Sci Rep / Year: 2017
Title: Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator.
Authors: Kromann-Hansen, T. / Louise Lange, E. / Peter Srensen, H. / Hassanzadeh-Ghassabeh, G. / Huang, M. / Jensen, J.K. / Muyldermans, S. / Declerck, P.J. / Komives, E.A. / Andreasen, P.A.
History
DepositionJul 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Urokinase-type plasminogen activator
A: Urokinase-type plasminogen activator
C: Urokinase-type plasminogen activator
D: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,22016
Polymers110,2174
Non-polymers1,00312
Water00
1
B: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8054
Polymers27,5541
Non-polymers2513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8054
Polymers27,5541
Non-polymers2513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8645
Polymers27,5541
Non-polymers3104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7463
Polymers27,5541
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.700, 194.700, 37.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Urokinase-type plasminogen activator / uPA


Mass: 27554.158 Da / Num. of mol.: 4 / Mutation: C122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plau / Production host: Escherichia coli (E. coli) / References: UniProt: P06869, u-plasminogen activator
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100 mM HEPES, 1.8 M LisSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 3.05→38.68 Å / Num. obs: 29462 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.91
Reflection shellResolution: 3.05→3.15 Å / Rmerge(I) obs: 0.661

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVA

4dva


Resolution: 3.047→38.683 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 1471 4.99 %
Rwork0.2134 --
obs0.2156 29461 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.047→38.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 44 0 7056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057260
X-RAY DIFFRACTIONf_angle_d1.1749804
X-RAY DIFFRACTIONf_dihedral_angle_d14.1492648
X-RAY DIFFRACTIONf_chiral_restr0.0521012
X-RAY DIFFRACTIONf_plane_restr0.0071256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0473-3.14570.32121330.2972543X-RAY DIFFRACTION98
3.1457-3.2580.35331350.27442565X-RAY DIFFRACTION100
3.258-3.38840.34041360.2732579X-RAY DIFFRACTION100
3.3884-3.54250.3481340.26832554X-RAY DIFFRACTION99
3.5425-3.72910.30761350.24692573X-RAY DIFFRACTION98
3.7291-3.96260.30231320.22322496X-RAY DIFFRACTION98
3.9626-4.26820.24641320.1772519X-RAY DIFFRACTION98
4.2682-4.6970.18631360.16612570X-RAY DIFFRACTION98
4.697-5.37510.22871340.16892563X-RAY DIFFRACTION98
5.3751-6.76620.22031330.2072534X-RAY DIFFRACTION99
6.7662-38.68610.23811310.21932494X-RAY DIFFRACTION96

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