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- PDB-5xvp: E. fae Cas1-Cas2/prespacer/target ternary complex revealing the f... -

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Basic information

Entry
Database: PDB / ID: 5xvp
TitleE. fae Cas1-Cas2/prespacer/target ternary complex revealing the fully integrated states
Components
  • (CRISPR-associated ...) x 2
  • (DNA (73-MER)) x 2
  • DNA (5'-D(P*TP*TP*CP*TP*CP*CP*GP*AP*G)-3')
KeywordsIMMUNE SYSTEM / CRISPR / Cas
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, NMENI subtype / CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1
Similarity search - Domain/homology
DNA / DNA (> 10) / CRISPR-associated endoribonuclease Cas2 / CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesEnterococcus faecalis TX0027 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsXiao, Y. / Ng, S. / Nam, K.H. / Ke, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
CitationJournal: Nature / Year: 2017
Title: How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration.
Authors: Xiao, Y. / Ng, S. / Hyun Nam, K. / Ke, A.
History
DepositionJun 28, 2017Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 12, 2022Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
G: DNA (73-MER)
H: DNA (73-MER)
I: DNA (5'-D(P*TP*TP*CP*TP*CP*CP*GP*AP*G)-3')
J: DNA (5'-D(P*TP*TP*CP*TP*CP*CP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,34212
Polymers210,29310
Non-polymers492
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38010 Å2
ΔGint-260 kcal/mol
Surface area73760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.870, 212.294, 512.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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CRISPR-associated ... , 2 types, 6 molecules ABCDEF

#1: Protein
CRISPR-associated endonuclease Cas1


Mass: 33492.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis TX0027 (bacteria)
Gene: cas1, HMPREF9501_02814 / Production host: Escherichia coli (E. coli)
References: UniProt: E6GPD7, Hydrolases; Acting on ester bonds
#2: Protein CRISPR-associated endoribonuclease Cas2


Mass: 12977.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis TX0027 (bacteria)
Gene: cas2, HMPREF9501_02813 / Production host: Escherichia coli (E. coli)
References: UniProt: E6GPD6, Hydrolases; Acting on ester bonds

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DNA chain , 3 types, 4 molecules GHIJ

#3: DNA chain DNA (73-MER)


Mass: 22406.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria)
#4: DNA chain DNA (73-MER)


Mass: 22548.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria)
#5: DNA chain DNA (5'-D(P*TP*TP*CP*TP*CP*CP*GP*AP*G)-3')


Mass: 2706.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria)

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.24 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate, 100 mM sodium citrate, pH 4.8, and 4-7% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 68246 / % possible obs: 99.1 % / Redundancy: 5.1 % / Net I/σ(I): 8.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementResolution: 3→49.03 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 41.415 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23264 3549 5 %RANDOM
Rwork0.19365 ---
obs0.19557 68098 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.857 Å2
Baniso -1Baniso -2Baniso -3
1--3.95 Å20 Å20 Å2
2--0.05 Å20 Å2
3---3.9 Å2
Refinement stepCycle: 1 / Resolution: 3→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11138 3251 2 2 14393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01714998
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212547
X-RAY DIFFRACTIONr_angle_refined_deg1.581.74920917
X-RAY DIFFRACTIONr_angle_other_deg1.413329140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8551350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67723.881572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.098152126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5341584
X-RAY DIFFRACTIONr_chiral_restr0.0850.22181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214343
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023186
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it15.3677.0095418
X-RAY DIFFRACTIONr_mcbond_other15.3657.0095417
X-RAY DIFFRACTIONr_mcangle_it19.70410.516762
X-RAY DIFFRACTIONr_mcangle_other19.70410.516763
X-RAY DIFFRACTIONr_scbond_it15.17.2649580
X-RAY DIFFRACTIONr_scbond_other15.0977.2649579
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other19.18710.76514156
X-RAY DIFFRACTIONr_long_range_B_refined21.76779.54518754
X-RAY DIFFRACTIONr_long_range_B_other21.76879.54318755
X-RAY DIFFRACTIONr_rigid_bond_restr16.345327544
X-RAY DIFFRACTIONr_sphericity_free23.85651
X-RAY DIFFRACTIONr_sphericity_bonded39.673526939
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 214 -
Rwork0.322 5019 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16250.04320.01080.3470.05070.00840.00410.0811-0.01380.0568-0.00620.013-0.00740.00430.00210.41480.030.0370.11360.01050.008716.98751.2402107.2047
20.384-0.1199-0.00130.0666-0.12610.83710.04440.0484-0.00610.02870.0078-0.0093-0.1848-0.123-0.05220.34260.04470.01540.0798-0.00290.042913.153223.6385128.4949
30.1217-0.02180.03230.1150.01220.0124-0.0048-0.0076-0.01210.01390.0148-0.004-0.0090.0043-0.010.2807-0.00140.00770.1552-0.00190.041355.475633.272244.7721
40.3917-0.06140.04040.1406-0.16140.20730.00460.0559-0.0583-0.00230.02310.0260.00490.0205-0.02770.26270.0034-0.00880.1505-0.01110.011433.793818.230921.4197
50.3287-0.0077-0.08730.3104-0.310.3413-0.0185-0.02680.02880.01160.0051-0.01250.0131-0.01410.01340.29470.0010.02420.1353-0.01380.045229.443825.836865.7022
60.37610.0126-0.07710.15110.13280.15970.09450.0096-0.04320.0343-0.0735-0.0248-0.0096-0.0054-0.0210.3414-0.01980.01610.1843-0.00060.051325.618126.866484.9328
70.02330.02360.00250.0589-0.00420.0136-0.00890.020.01220.0151-0.0016-0.0014-0.0228-0.03450.01050.29440.02890.00940.17310.00140.018226.019928.908970.4869
80.06690.04780.01850.0961-0.09780.2473-0.01820.00860.01320.0204-0.00940.0037-0.044-0.04080.02760.28530.04070.02090.1348-0.01520.010430.208226.277781.0559
90.03730.1107-0.06520.3894-0.22510.13220.04210.0152-0.02720.385-0.0354-0.0538-0.2248-0.021-0.00670.4980.0079-0.02380.179-0.03090.05543.899312.4783140.6014
100.2004-0.8158-0.54943.36912.23221.5209-0.0374-0.02650.03420.27170.0967-0.10350.07910.0582-0.05920.27430.03180.01950.16830.0340.165610.380539.905611.7322
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 286
2X-RAY DIFFRACTION2B1 - 288
3X-RAY DIFFRACTION3C1 - 288
4X-RAY DIFFRACTION4D1 - 288
5X-RAY DIFFRACTION5E4 - 107
6X-RAY DIFFRACTION6F4 - 105
7X-RAY DIFFRACTION7G2 - 72
8X-RAY DIFFRACTION8H3 - 73
9X-RAY DIFFRACTION9I1 - 9
10X-RAY DIFFRACTION10J2 - 9

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