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- PDB-1qrz: CATALYTIC DOMAIN OF PLASMINOGEN -

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Basic information

Entry
Database: PDB / ID: 1qrz
TitleCATALYTIC DOMAIN OF PLASMINOGEN
ComponentsPLASMINOGEN
KeywordsHYDROLASE / MICROPLASMINOGEN / SERINE PROTEASE / ZYMOGEN / CHYMOTRYPSIN FAMILY
Function / homology
Function and homology information


plasmin / tissue remodeling / protein antigen binding / Signaling by PDGF / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / Dissolution of Fibrin Clot / biological process involved in interaction with symbiont / Activation of Matrix Metalloproteinases / apolipoprotein binding ...plasmin / tissue remodeling / protein antigen binding / Signaling by PDGF / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / Dissolution of Fibrin Clot / biological process involved in interaction with symbiont / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of cell-substrate adhesion / 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 / 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 / protein domain specific binding / external side of plasma membrane / signaling receptor binding / negative regulation of cell population proliferation / serine-type endopeptidase activity / 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 / SYNCHROTRON / Resolution: 2 Å
AuthorsPeisach, E. / Wang, J. / de los Santos, T. / Reich, E. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal structure of the proenzyme domain of plasminogen.
Authors: Peisach, E. / Wang, J. / de los Santos, T. / Reich, E. / Ringe, D.
#1: Journal: Structure / Year: 1995
Title: The Crystal Structure of the Catalytic Domain of Human Urokinase-Type Plasminogen Activator
Authors: Spraggon, G.S. / Phillips, C. / Nowak, U.K. / Ponting, C.P. / Saunders, D. / Dobson, C.M. / Stuart, D.I. / Jones, E.Y.
#2: Journal: Nat.Struct.Biol. / Year: 1998
Title: The ternary microplasmin-staphylokinase-microplasmin complex is a proteinase- cofactor-substrate complex in action
Authors: Parry, M.A. / Fernandez-Catalan, C. / Bergner, A. / Huber, R. / Hopfner, K.P. / Schlott, B. / Guhrs, K.H. / Bode, W.
#3: Journal: Science / Year: 1998
Title: Crystal structure of the catalytic domain of human plasmin complexed with streptokinase
Authors: Wang, X. / Lin, X. / Loy, J.A. / Tang, J. / Zhang, X.C.
History
DepositionJun 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 25, 2013Group: Derived calculations
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: PLASMINOGEN
B: PLASMINOGEN
C: PLASMINOGEN
D: PLASMINOGEN


Theoretical massNumber of molelcules
Total (without water)108,0804
Polymers108,0804
Non-polymers00
Water9,170509
1
A: PLASMINOGEN


Theoretical massNumber of molelcules
Total (without water)27,0201
Polymers27,0201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PLASMINOGEN


Theoretical massNumber of molelcules
Total (without water)27,0201
Polymers27,0201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PLASMINOGEN


Theoretical massNumber of molelcules
Total (without water)27,0201
Polymers27,0201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PLASMINOGEN


Theoretical massNumber of molelcules
Total (without water)27,0201
Polymers27,0201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.658, 73.575, 81.363
Angle α, β, γ (deg.)90.00, 108.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PLASMINOGEN


Mass: 27020.016 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN / Mutation: M585Q, V673M, M788L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00747
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ISOPROPANOL, CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMbenzamidine1drop
3100 mMsodium cacodylate1drop
43 %2-propanol1reservoir
53 %PEG40001reservoir
620 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9924
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9924 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 63217 / Num. obs: 63217 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 3.6 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 11
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.631 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 199470

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2→35 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 95413.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD TARGET FUNCTION
RfactorNum. reflection% reflection
Rfree0.294 2869 4.9 %
Rwork0.235 --
all0.237 61073 -
obs0.235 58204 94.1 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.27 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20.75 Å2
2--0.65 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7588 0 0 509 8097
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.762.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 444 5 %
Rwork0.301 8385 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.371 / % reflection Rfree: 5 % / Rfactor Rwork: 0.301

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