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- PDB-3zth: Crystal structure of Stu0660 of Streptococcus thermophilus -

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Basic information

Entry
Database: PDB / ID: 3zth
TitleCrystal structure of Stu0660 of Streptococcus thermophilus
ComponentsSTU0660
KeywordsDNA BINDING / CRISPR / CAS
Function / homologyCRISPR-associated protein Csn2 subfamily St / CRISPR-associated protein Csn2 subfamily St / metal ion binding / CRISPR-associated protein Cas7
Function and homology information
Biological speciesSTREPTOCOCCUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLee, K.-H. / Robinson, H. / Oh, B.-H.
CitationJournal: Proteins / Year: 2012
Title: Identification, Structural, and Biochemical Characterization of a Group of Large Csn2 Proteins Involved in Crispr-Mediated Bacterial Immunity.
Authors: Lee, K.-H. / Lee, S.-G. / Lee, K.E. / Jeon, H. / Robinson, H. / Oh, B.-H.
History
DepositionJul 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references / Source and taxonomy
Revision 1.2Oct 31, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STU0660
B: STU0660
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1424
Polymers84,0932
Non-polymers492
Water4,306239
1
A: STU0660
B: STU0660
hetero molecules

A: STU0660
B: STU0660
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,2848
Polymers168,1874
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area23830 Å2
ΔGint-190 kcal/mol
Surface area61100 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-50.4 kcal/mol
Surface area36110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.149, 101.869, 102.784
Angle α, β, γ (deg.)90.00, 115.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein STU0660


Mass: 42046.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS THERMOPHILUS (bacteria) / Strain: LMG 18311 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q5M539
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.6 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 80761 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Rsym value: 0.084 / Net I/σ(I): 27.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.246 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 3887 4.6 %RANDOM
Rwork0.2046 ---
obs0.2046 80761 98.9 %-
Solvent computationBsol: 35.0677 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.903 Å20 Å2-12.67 Å2
2--2.515 Å20 Å2
3----5.417 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5834 0 2 239 6075
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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: 2.4→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.246 2091 -
obs--97 %

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