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- PDB-1c76: STAPHYLOKINASE (SAK) MONOMER -

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Basic information

Entry
Database: PDB / ID: 1c76
TitleSTAPHYLOKINASE (SAK) MONOMER
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: 2.25 Å
AuthorsRao, Z. / Jiang, F. / Liu, Y. / Zhang, X. / Chen, Y. / Bartlam, M. / Song, H. / Ding, Y.
CitationJournal: To be published
Title: Crystal Structure of Staphylokinase Dimer Offers New Clue to Reduction of Immunogenicity
Authors: Rao, Z. / Jiang, F. / Liu, Y. / Zhang, X. / Chen, Y. / Bartlam, M. / Song, H. / Ding, Y.
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

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Assembly

Deposited unit
A: STAPHYLOKINASE


Theoretical massNumber of molelcules
Total (without water)15,4881
Polymers15,4881
Non-polymers00
Water28816
1
A: STAPHYLOKINASE

A: STAPHYLOKINASE


Theoretical massNumber of molelcules
Total (without water)30,9752
Polymers30,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
Unit cell
Length a, b, c (Å)43.92, 59.84, 102.88
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P68802, aureolysin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, pH 8.0, vapor diffusion/hanging drop, temperature 293K

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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 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 6589 / Num. obs: 6589 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.8
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.182 / Num. unique all: 803 / % possible all: 97.6

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.25→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.273 672 -
Rwork0.201 --
all0.206 6137 -
obs0.216 6400 91.3 %
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 0 16 997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.01

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