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- PDB-1c78: STAPHYLOKINASE (SAK) DIMER -

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Basic information

Entry
Database: PDB / ID: 1c78
TitleSTAPHYLOKINASE (SAK) DIMER
ComponentsSTAPHYLOKINASE
KeywordsHYDROLASE / BETA-GRASP FAMILY
Function / homologyUbiquitin-like (UB roll) - #130 / Staphylokinase / Staphylokinase/Streptokinase superfamily / Staphylokinase/Streptokinase family / Ubiquitin-like (UB roll) / Roll / extracellular region / Alpha Beta / Staphylokinase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsRao, Z. / Jiang, F. / Liu, Y. / Zhang, X. / Chen, Y. / Bartlam, M. / Song, H. / Ding, Y.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Crystal structure of a staphylokinase: variant a model for reduced antigenicity.
Authors: Chen, Y. / Song, G. / Jiang, F. / Feng, L. / Zhang, X. / Ding, Y. / Bartlam, M. / Yang, A. / Ma, X. / Ye, S. / Liu, Y. / Tang, H. / Song, H. / Rao, Z.
History
DepositionFeb 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: STAPHYLOKINASE
B: STAPHYLOKINASE


Theoretical massNumber of molelcules
Total (without water)30,9752
Polymers30,9752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.87, 59.26, 102.42
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsIt is proposed in the primary citation that the biological unit is a "head-to-tail" dimer (pdb entry 1c77). Two other dimers have been considered, with alpha helices at the interface (1c78) and beta sheets at the interface (1c79) respectively. However, the "head-to-tail" dimer interface allows for the formation of strong hydrophobic interactions as well as hydrogen bonds and is more stable than the other two forms. The authors have experimental evidence from site direct mutagenesis which supports their proposition.

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Components

#1: Protein STAPHYLOKINASE / SAK


Mass: 15487.585 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: VPET-11 / Production host: Escherichia coli (E. coli) / References: UniProt: P68802, aureolysin

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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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 1000, pH 8.5, vapor diffusion/hanging drop, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 mMTris-HCl1drop
345-50 %(w/v)PEG10001reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 12320 / Num. obs: 12320 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 10.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.174 / Num. unique all: 1476 / % possible all: 99.5
Reflection
*PLUS
Num. obs: 12387 / % possible obs: 99.8 % / Num. measured all: 48705 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.204

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.267 1147 -
Rwork0.198 --
all0.207 11210 -
obs0.204 11954 90.5 %
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 0 0 2084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0185
X-RAY DIFFRACTIONc_angle_deg1.98
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11959 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.07

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