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- PDB-1qqr: CRYSTAL STRUCTURE OF STREPTOKINASE DOMAIN B -

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Basic information

Entry
Database: PDB / ID: 1qqr
TitleCRYSTAL STRUCTURE OF STREPTOKINASE DOMAIN B
ComponentsSTREPTOKINASE DOMAIN B
KeywordsHYDROLASE ACTIVATOR / NON-PROTEOLYTIC / PLASMINOGEN ACTIVATION / FIBRINOLYSIS
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Ubiquitin-like (UB roll) - #180 / Streptokinase / Staphylokinase / Staphylokinase/Streptokinase superfamily / Staphylokinase/Streptokinase family / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus dysgalactiae subsp. equisimilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSpraggon, G. / Zhang, X.X. / Ponting, C.P. / Fox, V.F. / Phillips, C. / Smith, R.A.G. / Jones, E.Y. / Dobson, C. / Stuart, D.I.
CitationJournal: To be Published
Title: Crystal Structure of Streptokinse Domain B
Authors: Spraggon, G. / Zhang, X.X. / Ponting, C.P. / Fox, V.F. / Phillips, C. / Smith, R.A.G. / Jones, E.Y. / Dobson, C. / Stuart, D.I.
History
DepositionJun 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STREPTOKINASE DOMAIN B
B: STREPTOKINASE DOMAIN B
C: STREPTOKINASE DOMAIN B
D: STREPTOKINASE DOMAIN B


Theoretical massNumber of molelcules
Total (without water)64,0884
Polymers64,0884
Non-polymers00
Water6,071337
1
A: STREPTOKINASE DOMAIN B


Theoretical massNumber of molelcules
Total (without water)16,0221
Polymers16,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STREPTOKINASE DOMAIN B


Theoretical massNumber of molelcules
Total (without water)16,0221
Polymers16,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: STREPTOKINASE DOMAIN B


Theoretical massNumber of molelcules
Total (without water)16,0221
Polymers16,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: STREPTOKINASE DOMAIN B


Theoretical massNumber of molelcules
Total (without water)16,0221
Polymers16,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.870, 93.780, 156.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein
STREPTOKINASE DOMAIN B


Mass: 16021.934 Da / Num. of mol.: 4 / Fragment: B-DOMAIN / Source method: isolated from a natural source
Source: (natural) Streptococcus dysgalactiae subsp. equisimilis (bacteria)
Species: Streptococcus dysgalactiae / Strain: subsp. equisimilis / References: UniProt: P00779
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.9 Å3/Da / Density % sol: 57.63 %

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 34029 / Num. obs: 31237 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.078

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Processing

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

1bml


Resolution: 2.3→50 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD REFINEMENT
RfactorNum. reflection% reflection
Rfree0.2417 1564 5 %
Rwork0.1968 --
obs0.1968 31237 91.8 %
all-34029 -
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.098 Å2 / ksol: 0.35326 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.52 Å20 Å20 Å2
2--6.65 Å20 Å2
3---2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 0 0 337 4794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.6
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 171 4.9 %
Rwork0.261 3286 -
obs--62.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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