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- PDB-1rjx: Human PLASMINOGEN CATALYTIC DOMAIN, K698M MUTANT -

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Basic information

Entry
Database: PDB / ID: 1rjx
TitleHuman PLASMINOGEN CATALYTIC DOMAIN, K698M MUTANT
ComponentsPlasminogen
KeywordsHYDROLASE / microplasminogen / plasminogen activation / streptokinase
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / myoblast differentiation / labyrinthine layer blood vessel development / biological process involved in interaction with symbiont / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of fibrinolysis / negative regulation of cell-substrate adhesion / positive regulation of blood vessel endothelial cell migration / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / protein processing / 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 / endopeptidase activity / blood microparticle / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / 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 ...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 / Serine proteases, trypsin family, histidine 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTerzyan, S. / Wakeham, N. / Zhai, P. / Rodgers, K. / Zhang, X.C.
CitationJournal: Proteins / Year: 2004
Title: Characterization of Lys-698 to met substitution in human plasminogen catalytic domain
Authors: Terzyan, S. / Wakeham, N. / Zhai, P. / Rodgers, K. / Zhang, X.C.
History
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8069
Polymers27,0371
Non-polymers7698
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasminogen
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)667,334216
Polymers648,88924
Non-polymers18,444192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_676z+1,-x+2,-y+11
crystal symmetry operation7_674-z+1,-x+2,y-11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_766-y+2,z+1,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_764-y+2,-z+1,x-11
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_775-y+2,-x+2,-z1
crystal symmetry operation15_575y,-x+2,z1
crystal symmetry operation16_755-y+2,x,z1
crystal symmetry operation17_566x,z+1,-y+11
crystal symmetry operation18_764-x+2,z+1,y-11
crystal symmetry operation19_766-x+2,-z+1,-y+11
crystal symmetry operation20_564x,-z+1,y-11
crystal symmetry operation21_656z+1,y,-x+11
crystal symmetry operation22_674z+1,-y+2,x-11
crystal symmetry operation23_654-z+1,y,x-11
crystal symmetry operation24_676-z+1,-y+2,-x+11
Buried area101100 Å2
ΔGint-2928 kcal/mol
Surface area192110 Å2
MethodPISA
3
B: Plasminogen
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)166,83354
Polymers162,2226
Non-polymers4,61148
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation38_665-y+3/2,-x+3/2,-z+1/21
crystal symmetry operation42_654-x+3/2,z+1/2,y-1/21
crystal symmetry operation46_564z+1/2,-y+3/2,x-1/21
MethodPQS
Unit cell
Length a, b, c (Å)158.396, 158.396, 158.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Plasminogen


Mass: 27037.061 Da / Num. of mol.: 1 / Fragment: Serine Protease CATALYTIC DOMAIN / Mutation: K698M, R561A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: PLG / Plasmid: pet11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00747, plasmin
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.06 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 5.6
Details: Li2SO4, Na citrate, pH 5.6, hanging drop, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
30.4 Murea1drop
41.0 M1reservoirLi2SO4
50.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2002 / Details: Blue Osmic optics
RadiationMonochromator: Osmic optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→45.725 Å / Num. obs: 15398 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 22.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3 / Num. unique all: 1507 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.32 Å / Lowest resolution: 50 Å
Reflection shell
*PLUS
Highest resolution: 2.32 Å / % possible obs: 100 % / Num. unique obs: 1507

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDJ

1ddj


Resolution: 2.3→45.725 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1058 6 %RANDOM
Rwork0.194 ---
all-16771 --
obs-14771 95 %-
Solvent computationBsol: 57.8587 Å2 / ksol: 0.373242 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 40 153 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0117
X-RAY DIFFRACTIONc_angle_deg1.63716
X-RAY DIFFRACTIONx_mcbond_it2.11.5
X-RAY DIFFRACTIONx_mcangle_it3.4982
X-RAY DIFFRACTIONx_scbond_it2.732
X-RAY DIFFRACTIONx_scangle_it3.92.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2water.topwater_rep.param
X-RAY DIFFRACTION3ion.topion.param
Refinement
*PLUS
Rfactor Rfree: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.73

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