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- PDB-2sak: STAPHYLOKINASE (SAKSTAR VARIANT) -

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Basic information

Entry
Database: PDB / ID: 2sak
TitleSTAPHYLOKINASE (SAKSTAR VARIANT)
ComponentsSTAPHYLOKINASE
KeywordsPLASMINOGEN ACTIVATOR / PLASMINOGEN ACTIVATION / FIBRINOLYSIS / STAPHYLOKINASE / HYDROLASE
Function / homology
Function and homology information


symbiont-mediated activation of host plasminogen / symbiont-mediated suppression of host complement activation by activation of host proteases / extracellular region
Similarity search - Function
Ubiquitin-like (UB roll) - #130 / Staphylokinase / Staphylokinase/Streptokinase superfamily / Staphylokinase/Streptokinase family / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsRabijns, A. / De Bondt, H.L. / De Maeyer, M. / Lasters, I. / De Ranter, C.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Three-dimensional structure of staphylokinase, a plasminogen activator with therapeutic potential.
Authors: Rabijns, A. / De Bondt, H.L. / De Ranter, C.
History
DepositionFeb 20, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: STAPHYLOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0212
Polymers13,8991
Non-polymers1221
Water1,53185
1
A: STAPHYLOKINASE
hetero molecules

A: STAPHYLOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0424
Polymers27,7982
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)60.600, 43.730, 54.270
Angle α, β, γ (deg.)90.00, 115.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein STAPHYLOKINASE


Mass: 13898.865 Da / Num. of mol.: 1 / Mutation: SAKSTAR VARIANT / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P68802
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.2M MGCL2, O.1M TRIS BUFFER PH 8.5 AND 30 % PEG 4K, USING MICROSEEDING TECHNIQUES.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: Rabijins, A., (1997) Protein.Struct.Funct.Genet., 27, 160.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 M1dropMgCl2
20.05 MTris-HCl1drop
317.5 %PEG40001drop
417.5 mg/mlprotein1drop
525 mMHEPES1drop
60.2 M1reservoirMgCl2
70.1 MTris-HCl1reservoir
835 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 11949 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.034 / Net I/σ(I): 25
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 8.5 / Rsym value: 0.119 / % possible all: 100
Reflection
*PLUS
Num. measured all: 76483 / Rmerge(I) obs: 0.034

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1199 9.6 %RANDOM
Rwork0.181 ---
obs0.181 11547 95.8 %-
Displacement parametersBiso mean: 19.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 8 85 1076
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.95
X-RAY DIFFRACTIONx_mcangle_it3.63
X-RAY DIFFRACTIONx_scbond_it4.51
X-RAY DIFFRACTIONx_scangle_it6.46
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3 127 9.5 %
Rwork0.26 1207 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.WATTOPH11.WAT
X-RAY DIFFRACTION3TRS.PARTRS.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.42
LS refinement shell
*PLUS
Rfactor Rfree: 0.3

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