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- PDB-4p6i: Crystal structure of the Cas1-Cas2 complex from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 4p6i
TitleCrystal structure of the Cas1-Cas2 complex from Escherichia coli
Components
  • CRISPR-associated endonuclease Cas1
  • CRISPR-associated endoribonuclease Cas2
KeywordsHYDROLASE / CRISPR-associated proteins / nuclease
Function / homology
Function and homology information


CRISPR-cas system / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA repair / DNA damage response / protein homodimerization activity ...CRISPR-cas system / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA repair / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
CRISPR-associated protein Cas2 subtype / CRISPR-associated protein (Cas_Cas2CT1978) / CRISPR-associated protein Cas1, ECOLI subtype / CRISPR-associated protein Cas1, type I-E / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 ...CRISPR-associated protein Cas2 subtype / CRISPR-associated protein (Cas_Cas2CT1978) / CRISPR-associated protein Cas1, ECOLI subtype / CRISPR-associated protein Cas1, type I-E / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas2 / CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsNunez, J.K. / Kranzusch, P.J. / Noeske, J. / Doudna, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1244557 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.
Authors: Nunez, J.K. / Kranzusch, P.J. / Noeske, J. / Wright, A.V. / Davies, C.W. / Doudna, J.A.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Jan 7, 2015Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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: CRISPR-associated endoribonuclease Cas2
B: CRISPR-associated endoribonuclease Cas2
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endonuclease Cas1
F: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)156,0486
Polymers156,0486
Non-polymers00
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15400 Å2
ΔGint-99 kcal/mol
Surface area55010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.875, 125.696, 99.306
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR-associated endoribonuclease Cas2


Mass: 11553.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ygbF, cas2, b2754, JW5438 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45956, Hydrolases; Acting on ester bonds
#2: Protein
CRISPR-associated endonuclease Cas1


Mass: 33235.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2755, cas1, JW2725, pstS, ygbT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46896, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 150 mM NaCl, 5% w/v PEG 8000, 100 mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.3→62.85 Å / Num. obs: 97929 / % possible obs: 97.22 % / Redundancy: 3.1 % / Net I/σ(I): 9.19
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1 / % possible all: 91.21

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→62.848 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 2010 2.06 %5
Rwork0.2254 ---
obs0.2258 97798 97.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→62.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9925 0 0 525 10450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310116
X-RAY DIFFRACTIONf_angle_d0.61713731
X-RAY DIFFRACTIONf_dihedral_angle_d10.4413760
X-RAY DIFFRACTIONf_chiral_restr0.0421584
X-RAY DIFFRACTIONf_plane_restr0.0031773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35790.39491330.33766192X-RAY DIFFRACTION88
2.3579-2.42160.32731430.31276992X-RAY DIFFRACTION99
2.4216-2.49290.33261540.2926947X-RAY DIFFRACTION99
2.4929-2.57330.2841530.28546951X-RAY DIFFRACTION99
2.5733-2.66530.3381370.28956869X-RAY DIFFRACTION98
2.6653-2.7720.3661280.30436764X-RAY DIFFRACTION96
2.772-2.89820.27381510.25436973X-RAY DIFFRACTION100
2.8982-3.0510.2621460.23977014X-RAY DIFFRACTION100
3.051-3.24210.27111450.23787024X-RAY DIFFRACTION100
3.2421-3.49240.25871450.24236715X-RAY DIFFRACTION95
3.4924-3.84390.26161380.22526551X-RAY DIFFRACTION93
3.8439-4.40.20561410.1866623X-RAY DIFFRACTION94
4.4-5.5430.17791460.17167060X-RAY DIFFRACTION99
5.543-62.87140.17171500.17337113X-RAY DIFFRACTION99

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