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- PDB-5hpg: STRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DO... -

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Basic information

Entry
Database: PDB / ID: 5hpg
TitleSTRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DOMAIN OF HUMAN PLASMINOGEN
ComponentsPLASMINOGEN
KeywordsSERINE PROTEASE / KRINGLE 5 / HUMAN PLASMINOGEN / FIBRINOLYSIS
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / endopeptidase activity / blood microparticle / negative regulation of cell population proliferation / protein domain specific binding / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle ...Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsTulinsky, A. / Mochalkin, I. / Castellino, F.J.
CitationJournal: Biochemistry / Year: 1998
Title: Structure and ligand binding determinants of the recombinant kringle 5 domain of human plasminogen.
Authors: Chang, Y. / Mochalkin, I. / McCance, S.G. / Cheng, B. / Tulinsky, A. / Castellino, F.J.
History
DepositionSep 19, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASMINOGEN
B: PLASMINOGEN


Theoretical massNumber of molelcules
Total (without water)18,7892
Polymers18,7892
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.430, 79.200, 30.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.84721, -0.07401, -0.52607), (-0.03051, -0.98184, 0.18726), (-0.53037, 0.1747, 0.82957)
Vector: 31.749, 53.688, 3.802)

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Components

#1: Protein PLASMINOGEN


Mass: 9394.440 Da / Num. of mol.: 2 / Fragment: KRINGLE 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00747, plasmin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.51 Å3/Da / Density % sol: 42 %
Crystal growpH: 7
Details: 24% (W/V) PEG 8000, 0.1 M NA-HEPES, PH 7.0, 0.15 M LI2(SO4)
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
212 %(w/v)PEG80001drop
30.05 Msodium HEPES1drop
40.075 M1dropLi2SO4
524 %(w/v)PEG80001reservoir
60.1 Msodium HEPES1reservoir
70.15 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MSC-YALE MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.66→35.26 Å / Num. obs: 16720 / % possible obs: 72 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.042 / Rsym value: 0.051 / Net I/σ(I): 14
Reflection shellResolution: 1.6→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.13 / % possible all: 37
Reflection
*PLUS
Observed criterion σ(I): 1 / Num. measured all: 42366
Reflection shell
*PLUS
Highest resolution: 1.66 Å / Lowest resolution: 1.8 Å / % possible obs: 37 %

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Processing

Software
NameVersionClassification
RIGAKUR-AXISdata collection
RIGAKUR-AXISdata reduction
AMoREphasing
PROFFTrefinement
R-AXIS(RIGAKU)data reduction
R-AXIS(RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PKR

1pkr


Resolution: 1.66→7 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.166 --
all-16720 -
obs-15014 84 %
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 1.66→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 0 193 1489
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.8
X-RAY DIFFRACTIONp_multtor_nbd0.240.8
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.230.8
X-RAY DIFFRACTIONp_planar_tor5.23
X-RAY DIFFRACTIONp_staggered_tor17.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it1.41.5
X-RAY DIFFRACTIONp_scbond_it3.53
X-RAY DIFFRACTIONp_mcangle_it1.72
X-RAY DIFFRACTIONp_scangle_it4.13.5

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