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- PDB-6ke1: Crystal structure of TtCas1 -

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Basic information

Entry
Database: PDB / ID: 6ke1
TitleCrystal structure of TtCas1
ComponentsCRISPR-associated endonuclease Cas1 2
KeywordsDNA BINDING PROTEIN / CRISPR / Cas1
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, ECOLI subtype / CRISPR-associated protein Cas1, type I-E / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas1 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 Å
AuthorsWang, Y.L. / Li, J.Z. / Yang, J. / Wang, J.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630015 China
National Natural Science Foundation of China31725008 China
CitationJournal: Sci China Life Sci / Year: 2020
Title: Crystal structure of Cas1 in complex with branched DNA.
Authors: Yang, J. / Li, J. / Wang, J. / Sheng, G. / Wang, M. / Zhao, H. / Yang, Y. / Wang, Y.
History
DepositionJul 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1 2
B: CRISPR-associated endonuclease Cas1 2


Theoretical massNumber of molelcules
Total (without water)71,5302
Polymers71,5302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-23 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.432, 150.432, 219.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTYRTYR(chain 'A' and (resid 22 through 41 or resid 43...AA22 - 4022 - 40
12GLUGLUGLYGLY(chain 'A' and (resid 22 through 41 or resid 43...AA43 - 9543 - 95
13ARGARGPHEPHE(chain 'A' and (resid 22 through 41 or resid 43...AA98 - 12898 - 128
14PROPROTHRTHR(chain 'A' and (resid 22 through 41 or resid 43...AA131 - 137131 - 137
15GLNGLNGLUGLU(chain 'A' and (resid 22 through 41 or resid 43...AA140 - 145140 - 145
16ARGARGTRPTRP(chain 'A' and (resid 22 through 41 or resid 43...AA148 - 156148 - 156
17GLYGLYPROPRO(chain 'A' and (resid 22 through 41 or resid 43...AA161 - 163161 - 163
18ARGARGTYRTYR(chain 'A' and (resid 22 through 41 or resid 43...AA167 - 169167 - 169
19PROPROGLYGLY(chain 'A' and (resid 22 through 41 or resid 43...AA179 - 203179 - 203
110PROPROARGARG(chain 'A' and (resid 22 through 41 or resid 43...AA206 - 238206 - 238
111ALAALAALAALA(chain 'A' and (resid 22 through 41 or resid 43...AA241241
112GLUGLUARGARG(chain 'A' and (resid 22 through 41 or resid 43...AA245 - 252245 - 252
113ALAALAARGARG(chain 'A' and (resid 22 through 41 or resid 43...AA254 - 256254 - 256
114GLUGLUGLUGLU(chain 'A' and (resid 22 through 41 or resid 43...AA261261
115LEULEULEULEU(chain 'A' and (resid 22 through 41 or resid 43...AA264 - 275264 - 275
116ARGARGGLYGLY(chain 'A' and (resid 22 through 41 or resid 43...AA277 - 278277 - 278
217TYRTYRTYRTYR(chain 'B' and (resid 22 through 41 or resid 43...BB22 - 4022 - 40
218GLUGLUGLYGLY(chain 'B' and (resid 22 through 41 or resid 43...BB43 - 9543 - 95
219ARGARGPHEPHE(chain 'B' and (resid 22 through 41 or resid 43...BB98 - 12898 - 128
220PROPROTHRTHR(chain 'B' and (resid 22 through 41 or resid 43...BB131 - 137131 - 137
221GLNGLNGLUGLU(chain 'B' and (resid 22 through 41 or resid 43...BB140 - 145140 - 145
222ARGARGTRPTRP(chain 'B' and (resid 22 through 41 or resid 43...BB148 - 156148 - 156
223GLYGLYPROPRO(chain 'B' and (resid 22 through 41 or resid 43...BB161 - 163161 - 163
224ARGARGALAALA(chain 'B' and (resid 22 through 41 or resid 43...BB175 - 177175 - 177
225PROPROGLYGLY(chain 'B' and (resid 22 through 41 or resid 43...BB179 - 203179 - 203
226PROPROARGARG(chain 'B' and (resid 22 through 41 or resid 43...BB206 - 238206 - 238
227ALAALAALAALA(chain 'B' and (resid 22 through 41 or resid 43...BB241241
228GLUGLUARGARG(chain 'B' and (resid 22 through 41 or resid 43...BB245 - 252245 - 252
229ALAALAARGARG(chain 'B' and (resid 22 through 41 or resid 43...BB254 - 256254 - 256
230GLUGLUGLUGLU(chain 'B' and (resid 22 through 41 or resid 43...BB261261
231LEULEULEULEU(chain 'B' and (resid 22 through 41 or resid 43...BB264 - 275264 - 275
232LEULEUGLYGLY(chain 'B' and (resid 22 through 41 or resid 43...BB279 - 280279 - 280

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Components

#1: Protein CRISPR-associated endonuclease Cas1 2


Mass: 35765.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: cas1-2, TTHB193 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q53WG8, Hydrolases; Acting on ester bonds

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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: 5.01 Å3/Da / Density % sol: 75.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.8-2.3M NaCl, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 3.39→50 Å / Num. obs: 19271 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 127.99 Å2 / Rsym value: 0.093 / Net I/σ(I): 28.8
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 6.6 % / Num. unique obs: 953 / Rsym value: 0.71 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KDV

6kdv


Resolution: 3.39→42.6 Å / SU ML: 0.478 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2136
RfactorNum. reflection% reflection
Rfree0.2293 1002 5.2 %
Rwork0.2209 --
obs0.2212 19265 91.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 137.88 Å2
Refinement stepCycle: LAST / Resolution: 3.39→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 0 0 3824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393906
X-RAY DIFFRACTIONf_angle_d1.0165311
X-RAY DIFFRACTIONf_chiral_restr0.049594
X-RAY DIFFRACTIONf_plane_restr0.0069690
X-RAY DIFFRACTIONf_dihedral_angle_d7.3842275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.39-3.570.38031680.32012516X-RAY DIFFRACTION91.64
3.57-3.790.33221620.27242580X-RAY DIFFRACTION93.36
3.79-4.080.26251270.2272613X-RAY DIFFRACTION93.13
4.08-4.50.22071530.19842589X-RAY DIFFRACTION92.45
4.5-5.140.22911150.19092627X-RAY DIFFRACTION92.01
5.14-6.480.23721440.24882621X-RAY DIFFRACTION91.16
6.48-42.60.18341330.20572717X-RAY DIFFRACTION88.26
Refinement TLS params.Method: refined / Origin x: -37.2268332524 Å / Origin y: 47.4397948243 Å / Origin z: 7.16683108039 Å
111213212223313233
T1.03428647368 Å2-0.0310195400472 Å20.0489191756693 Å2-1.02935538127 Å2-0.0935507840629 Å2--1.05383159574 Å2
L2.68702312288 °2-0.111667485869 °2-0.409185447394 °2-2.29815781489 °2-1.09295063291 °2--1.31062493119 °2
S-0.157972352411 Å °-0.0316853928153 Å °-0.642707834414 Å °-0.196461764622 Å °0.164595496953 Å °0.150469959445 Å °-0.0614100602181 Å °-0.0222355494265 Å °-0.0492973376757 Å °
Refinement TLS groupSelection details: all

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