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- PDB-2i9a: Crystal structure of the free aminoterminal fragment of urokinase... -

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Basic information

Entry
Database: PDB / ID: 2i9a
TitleCrystal structure of the free aminoterminal fragment of urokinase type plasminogen activator (ATF)
ComponentsUrokinase-type plasminogen activatorUrokinase
KeywordsHYDROLASE / growth factor-like domain / kringle domain
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
Plasminogen Kringle 4 / Plasminogen Kringle 4 / Laminin / Laminin / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / Laminin / Laminin / 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 / Ribbon / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLubkowski, J. / Barinka, C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural basis of interaction between urokinase-type plasminogen activator and its receptor.
Authors: Barinka, C. / Parry, G. / Callahan, J. / Shaw, D.E. / Kuo, A. / Bdeir, K. / Cines, D.B. / Mazar, A. / Lubkowski, J.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,9748
Polymers65,5944
Non-polymers3804
Water6,503361
1
A: Urokinase-type plasminogen activator


Theoretical massNumber of molelcules
Total (without water)16,3981
Polymers16,3981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Urokinase-type plasminogen activator


Theoretical massNumber of molelcules
Total (without water)16,3981
Polymers16,3981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4932
Polymers16,3981
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6834
Polymers16,3981
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.603, 64.327, 64.623
Angle α, β, γ (deg.)107.62, 92.11, 95.75
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a monomer. There are 4 biological units in the asymmetric unit.

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Components

#1: Protein
Urokinase-type plasminogen activator / Urokinase


Mass: 16398.461 Da / Num. of mol.: 4 / Fragment: N-terminal fragment of urokinase, residues 21-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's S2 cells / References: UniProt: P00749, u-plasminogen activator
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 1.2 M sodium dihydrogen phosphate, 0.8 M potassium hydrogen phosphate, 200 mM lithium sulfate, 100 mM CHES, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.13539 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Jun 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13539 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 54650 / Num. obs: 54650 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.045 / Net I/σ(I): 19.63
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.58 / Num. unique all: 4899 / Rsym value: 0.221 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1URK

1urk


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.559 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20822 2757 5.1 %RANDOM
Rwork0.18153 ---
obs0.1829 51775 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.6 Å2-0.75 Å2
2--0.02 Å2-0.46 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 20 361 4278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214046
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.925493
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3365493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28723.333198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18615633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9551528
X-RAY DIFFRACTIONr_chiral_restr0.1150.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023152
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21690
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22759
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.52505
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54423939
X-RAY DIFFRACTIONr_scbond_it2.53431761
X-RAY DIFFRACTIONr_scangle_it3.814.51554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 159 -
Rwork0.257 3223 -
obs--82.13 %
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)
11.0149-0.0878-0.21953.20581.20021.9821-0.03140.0719-0.1471-0.2673-0.01790.2845-0.0365-0.06240.0492-0.11350.0018-0.025-0.1121-0.0054-0.04570.8976-21.567911.9219
21.3627-0.2424-0.71741.0650.38923.6435-0.1526-0.0321-0.0370.10650.0126-0.02470.13480.22990.14-0.1393-0.0249-0.0042-0.10440.0178-0.108413.923614.5811-12.586
31.7118-1.43650.46332.8025-0.63491.3353-0.0311-0.05220.12070.0468-0.0288-0.0907-0.01760.12010.0599-0.1341-0.01240.0143-0.098-0.0041-0.120623.8654-41.791817.0832
41.9408-0.65390.70951.3173-0.47731.97630.01240.00690.0707-0.04410.0239-0.0537-0.2062-0.0532-0.0363-0.1334-0.01810.0099-0.1502-0.0021-0.1215-8.8243.381627.0875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 13213 - 134
2X-RAY DIFFRACTION2BB11 - 13213 - 134
3X-RAY DIFFRACTION3CC11 - 13213 - 134
4X-RAY DIFFRACTION4DD11 - 13213 - 134

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