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- PDB-4duu: The X-ray Crystal Structure of Full-Length type I Human Plasminogen -

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Basic information

Entry
Database: PDB / ID: 4duu
TitleThe X-ray Crystal Structure of Full-Length type I Human Plasminogen
ComponentsPlasminogenPlasmin
KeywordsHYDROLASE / serine protease / fibrinolysis
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / 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 / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / 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. ...Peptidase S1A, plasmin / 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 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.2 Å
AuthorsLaw, R.H.P. / Caradoc-Davies, T. / Whisstock, J.C.
CitationJournal: Cell Rep / Year: 2012
Title: The X-ray crystal structure of full-length human plasminogen
Authors: Law, R.H.P. / Caradoc-Davies, T. / Cowieson, N. / Horvath, A.J. / Quek, A.J. / Encarnacao, J.A. / Steer, D. / Cowan, A. / Zhang, Q. / Lu, B.G.C. / Pike, R.N. / Smith, A.I. / Coughlin, P.B. / Whisstock, J.C.
History
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Structure summary
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasminogen


Theoretical massNumber of molelcules
Total (without water)88,5441
Polymers88,5441
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.120, 110.120, 234.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Plasminogen / Plasmin / serine protease


Mass: 88544.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: plasma / References: UniProt: P00747, plasmin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2M sodium formate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953697 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2011 / Details: Silicon mirrors (adaptive and U-bent)
RadiationMonochromator: Double crystal monochromator (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953697 Å / Relative weight: 1
ReflectionResolution: 5.2→99.7 Å / Num. obs: 5316 / % possible obs: 91.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 192.2 Å2 / Rmerge(I) obs: 0.174 / Rsym value: 0.078 / Net I/σ(I): 6.8
Reflection shellResolution: 5.2→5.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4134 / Rsym value: 0.361 / % possible all: 92.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DUR

4dur


Resolution: 5.2→27.97 Å / Cor.coef. Fo:Fc: 0.6437 / Cor.coef. Fo:Fc free: 0.5133 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.713 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3117 231 4.38 %RANDOM
Rwork0.2684 ---
obs0.2703 5275 88.61 %-
Displacement parametersBiso max: 291.54 Å2 / Biso mean: 89.2779 Å2 / Biso min: 46.12 Å2
Baniso -1Baniso -2Baniso -3
1--19.2461 Å20 Å20 Å2
2---19.2461 Å20 Å2
3---38.4921 Å2
Refine analyzeLuzzati coordinate error obs: 1.36 Å
Refinement stepCycle: LAST / Resolution: 5.2→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 0 35 5307
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1818SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes133HARMONIC2
X-RAY DIFFRACTIONt_gen_planes793HARMONIC5
X-RAY DIFFRACTIONt_it5431HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion698SEMIHARMONIC5
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_contact5207SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5431HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg7390HARMONIC20.82
X-RAY DIFFRACTIONt_omega_torsion0.93
X-RAY DIFFRACTIONt_other_torsion20.67
LS refinement shellResolution: 5.2→5.48 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2867 62 4.15 %
Rwork0.244 1433 -
all0.2457 1495 -
obs--88.61 %
Refinement TLS params.Method: refined / Origin x: 6.2245 Å / Origin y: -4.2719 Å / Origin z: 33.6256 Å
111213212223313233
T0.3809 Å20.029 Å2-0.1632 Å2-0.4328 Å2-0.039 Å2--0.3251 Å2
L0.2413 °2-0.8298 °2-0.9079 °2-2.6382 °22.5323 °2--2.714 °2
S-0.3649 Å °0.4757 Å °-0.1596 Å °-0.0751 Å °-0.0351 Å °0.5117 Å °-0.3374 Å °-0.3468 Å °0.4 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|791 A|801 - A|835 }A3 - 791
2X-RAY DIFFRACTION1{ A|3 - A|791 A|801 - A|835 }A801 - 835

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