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- PDB-4an8: Structure of Thermus thermophilus CasA (Cse1) -

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Basic information

Entry
Database: PDB / ID: 4an8
TitleStructure of Thermus thermophilus CasA (Cse1)
ComponentsCSE1
KeywordsIMMUNE SYSTEM / CRISPR / CASCADE / CASA
Function / homologyTopoisomerase I; Chain A, domain 4 - #100 / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / Topoisomerase I; Chain A, domain 4 / defense response to virus / Orthogonal Bundle / Mainly Alpha / ACETATE ION / CRISPR-associated protein CasA/Cse1
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSashital, D.G. / Wiedenheft, B. / Doudna, J.A.
CitationJournal: Mol.Cell / Year: 2012
Title: Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System.
Authors: Sashital, D.G. / Wiedenheft, B. / Doudna, J.A.
History
DepositionMar 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: CSE1
B: CSE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2685
Polymers113,0912
Non-polymers1773
Water6,269348
1
A: CSE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6633
Polymers56,5451
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CSE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6042
Polymers56,5451
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.360, 48.110, 129.780
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CSE1


Mass: 56545.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TEV PROTEASE SCAR AT N-TERMINUS (GAGS) / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Gene: TTHB188 / Plasmid: PSV272 (PET VECTOR WITH ADDED TEV PROTEASE SITE) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53VY1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5 / Details: 2.1M NAAC, MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.3→46.83 Å / Num. obs: 51896 / % possible obs: 99.6 % / Observed criterion σ(I): 2.5 / Redundancy: 3.9 % / Biso Wilson estimate: 36.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→46.825 Å / SU ML: 0.67 / σ(F): 1.99 / Phase error: 23.33 / Stereochemistry target values: ML
Details: CHAIN A RESIDUES 1-3, 130-143, 401-411 AND 497-502 ARE DISORDERED. CHAIN B RESIDUES 1-4, 129-143, 401-423 AND 494-502 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2472 2594 5 %
Rwork0.1959 --
obs0.1984 51896 99.59 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.448 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.2968 Å20 Å21.022 Å2
2--0.7999 Å20 Å2
3----1.0967 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7301 0 12 348 7661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097517
X-RAY DIFFRACTIONf_angle_d1.11910206
X-RAY DIFFRACTIONf_dihedral_angle_d14.1862842
X-RAY DIFFRACTIONf_chiral_restr0.0751102
X-RAY DIFFRACTIONf_plane_restr0.0061346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34180.31071280.25382433X-RAY DIFFRACTION96
2.3418-2.38680.30891350.24262582X-RAY DIFFRACTION100
2.3868-2.43560.28211360.23742571X-RAY DIFFRACTION100
2.4356-2.48850.26671360.23122587X-RAY DIFFRACTION100
2.4885-2.54640.30191360.22942595X-RAY DIFFRACTION100
2.5464-2.61010.27641350.23012552X-RAY DIFFRACTION100
2.6101-2.68060.30131370.22792607X-RAY DIFFRACTION100
2.6806-2.75950.29971350.22192557X-RAY DIFFRACTION100
2.7595-2.84860.29021370.21982607X-RAY DIFFRACTION100
2.8486-2.95040.30411360.21472594X-RAY DIFFRACTION100
2.9504-3.06850.25441350.20062565X-RAY DIFFRACTION100
3.0685-3.20810.22141390.18952630X-RAY DIFFRACTION100
3.2081-3.37720.22491360.18212582X-RAY DIFFRACTION100
3.3772-3.58870.23861360.18932588X-RAY DIFFRACTION100
3.5887-3.86570.21591370.17552611X-RAY DIFFRACTION100
3.8657-4.25450.22641380.17012618X-RAY DIFFRACTION100
4.2545-4.86950.20511390.16042641X-RAY DIFFRACTION100
4.8695-6.13290.24931390.19012643X-RAY DIFFRACTION100
6.1329-46.83480.2351440.20382739X-RAY DIFFRACTION99

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