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- PDB-6kdv: Crystal structure of TtCas1-DNA complex -

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Basic information

Entry
Database: PDB / ID: 6kdv
TitleCrystal structure of TtCas1-DNA complex
Components
  • CRISPR-associated endonuclease Cas1 2
  • DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*GP*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / CRISPR / Cas1 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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
DNA / DNA (> 10) / CRISPR-associated endonuclease Cas1 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.11 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 2, 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 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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
B: CRISPR-associated endonuclease Cas1 2
A: CRISPR-associated endonuclease Cas1 2
D: CRISPR-associated endonuclease Cas1 2
C: CRISPR-associated endonuclease Cas1 2
E: DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*GP*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
F: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')
G: DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*GP*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
H: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)172,0558
Polymers172,0558
Non-polymers00
Water00
1
B: CRISPR-associated endonuclease Cas1 2
A: CRISPR-associated endonuclease Cas1 2
G: DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*GP*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
H: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)86,0274
Polymers86,0274
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-69 kcal/mol
Surface area26780 Å2
MethodPISA
2
D: CRISPR-associated endonuclease Cas1 2
C: CRISPR-associated endonuclease Cas1 2
E: DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*GP*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
F: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)86,0274
Polymers86,0274
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-66 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.547, 201.199, 77.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERARGARG(chain 'A' and (resid 21 through 32 or resid 34...AB21 - 3221 - 32
121ALAALAGLUGLU(chain 'A' and (resid 21 through 32 or resid 34...AB34 - 8434 - 84
131ALAALAASPASP(chain 'A' and (resid 21 through 32 or resid 34...AB87 - 9687 - 96
141ALAALAVALVAL(chain 'A' and (resid 21 through 32 or resid 34...AB100 - 120100 - 120
151ARGARGARGARG(chain 'A' and (resid 21 through 32 or resid 34...AB122 - 125122 - 125
161ARGARGARGARG(chain 'A' and (resid 21 through 32 or resid 34...AB127127
171PROPROGLUGLU(chain 'A' and (resid 21 through 32 or resid 34...AB133 - 134133 - 134
181LEULEULEULEU(chain 'A' and (resid 21 through 32 or resid 34...AB138138
191VALVALLEULEU(chain 'A' and (resid 21 through 32 or resid 34...AB141 - 144141 - 144
1101GLYGLYSERSER(chain 'A' and (resid 21 through 32 or resid 34...AB146 - 157146 - 157
1111PROPROTRPTRP(chain 'A' and (resid 21 through 32 or resid 34...AB163 - 164163 - 164
1121TRPTRPTRPTRP(chain 'A' and (resid 21 through 32 or resid 34...AB174174
1131ALAALALYSLYS(chain 'A' and (resid 21 through 32 or resid 34...AB176 - 228176 - 228
1141TYRTYRGLUGLU(chain 'A' and (resid 21 through 32 or resid 34...AB231 - 242231 - 242
1151ALAALAGLUGLU(chain 'A' and (resid 21 through 32 or resid 34...AB246 - 248246 - 248
1161ARGARGGLNGLN(chain 'A' and (resid 21 through 32 or resid 34...AB250 - 260250 - 260
1171LEULEULEULEU(chain 'A' and (resid 21 through 32 or resid 34...AB264264
1181ARGARGARGARG(chain 'A' and (resid 21 through 32 or resid 34...AB267267
1191ALAALAGLYGLY(chain 'A' and (resid 21 through 32 or resid 34...AB269 - 278269 - 278
2201SERSERARGARG(chain 'B' and (resid 21 through 32 or resid 34...BA21 - 3221 - 32
2211ALAALAGLUGLU(chain 'B' and (resid 21 through 32 or resid 34...BA34 - 8434 - 84
2221ALAALAASPASP(chain 'B' and (resid 21 through 32 or resid 34...BA87 - 9687 - 96
2231ALAALAVALVAL(chain 'B' and (resid 21 through 32 or resid 34...BA100 - 120100 - 120
2241ARGARGARGARG(chain 'B' and (resid 21 through 32 or resid 34...BA122 - 125122 - 125
2251ARGARGARGARG(chain 'B' and (resid 21 through 32 or resid 34...BA127127
2261PROPROGLUGLU(chain 'B' and (resid 21 through 32 or resid 34...BA133 - 134133 - 134
2271LEULEULEULEU(chain 'B' and (resid 21 through 32 or resid 34...BA138138
2281VALVALLEULEU(chain 'B' and (resid 21 through 32 or resid 34...BA141 - 144141 - 144
2291GLYGLYSERSER(chain 'B' and (resid 21 through 32 or resid 34...BA146 - 157146 - 157
2301PROPROTRPTRP(chain 'B' and (resid 21 through 32 or resid 34...BA163 - 164163 - 164
2311TRPTRPTRPTRP(chain 'B' and (resid 21 through 32 or resid 34...BA174174
2321ALAALALYSLYS(chain 'B' and (resid 21 through 32 or resid 34...BA176 - 228176 - 228
2331TYRTYRGLUGLU(chain 'B' and (resid 21 through 32 or resid 34...BA231 - 242231 - 242
2341ALAALAGLUGLU(chain 'B' and (resid 21 through 32 or resid 34...BA246 - 248246 - 248
2351ARGARGGLNGLN(chain 'B' and (resid 21 through 32 or resid 34...BA250 - 260250 - 260
2361LEULEULEULEU(chain 'B' and (resid 21 through 32 or resid 34...BA264264
2371ARGARGARGARG(chain 'B' and (resid 21 through 32 or resid 34...BA267267
2381ALAALAGLYGLY(chain 'B' and (resid 21 through 32 or resid 34...BA269 - 278269 - 278
3391SERSERARGARG(chain 'C' and (resid 21 through 32 or resid 34...CD21 - 3221 - 32
3401ALAALAGLUGLU(chain 'C' and (resid 21 through 32 or resid 34...CD34 - 8434 - 84
3411ALAALAASPASP(chain 'C' and (resid 21 through 32 or resid 34...CD87 - 9687 - 96
3421ALAALAVALVAL(chain 'C' and (resid 21 through 32 or resid 34...CD100 - 120100 - 120
3431ARGARGARGARG(chain 'C' and (resid 21 through 32 or resid 34...CD122 - 125122 - 125
3441ARGARGARGARG(chain 'C' and (resid 21 through 32 or resid 34...CD127127
3451PROPROGLUGLU(chain 'C' and (resid 21 through 32 or resid 34...CD133 - 134133 - 134
3461LEULEULEULEU(chain 'C' and (resid 21 through 32 or resid 34...CD138138
3471VALVALLEULEU(chain 'C' and (resid 21 through 32 or resid 34...CD141 - 144141 - 144
3481GLYGLYSERSER(chain 'C' and (resid 21 through 32 or resid 34...CD146 - 157146 - 157
3491PROPROTRPTRP(chain 'C' and (resid 21 through 32 or resid 34...CD163 - 164163 - 164
3501TRPTRPTRPTRP(chain 'C' and (resid 21 through 32 or resid 34...CD174174
3511ALAALALYSLYS(chain 'C' and (resid 21 through 32 or resid 34...CD176 - 228176 - 228
3521TYRTYRGLUGLU(chain 'C' and (resid 21 through 32 or resid 34...CD231 - 242231 - 242
3531ALAALAGLUGLU(chain 'C' and (resid 21 through 32 or resid 34...CD246 - 248246 - 248
3541ARGARGGLNGLN(chain 'C' and (resid 21 through 32 or resid 34...CD250 - 260250 - 260
3551LEULEULEULEU(chain 'C' and (resid 21 through 32 or resid 34...CD264264
3561ARGARGARGARG(chain 'C' and (resid 21 through 32 or resid 34...CD267267
3571ALAALAGLYGLY(chain 'C' and (resid 21 through 32 or resid 34...CD269 - 278269 - 278
4581SERSERARGARG(chain 'D' and (resid 21 through 32 or resid 34...DC21 - 3221 - 32
4591ALAALAGLUGLU(chain 'D' and (resid 21 through 32 or resid 34...DC34 - 8434 - 84
4601ALAALAASPASP(chain 'D' and (resid 21 through 32 or resid 34...DC87 - 9687 - 96
4611ALAALAVALVAL(chain 'D' and (resid 21 through 32 or resid 34...DC100 - 120100 - 120
4621ARGARGARGARG(chain 'D' and (resid 21 through 32 or resid 34...DC122 - 125122 - 125
4631ARGARGARGARG(chain 'D' and (resid 21 through 32 or resid 34...DC127127
4641PROPROGLUGLU(chain 'D' and (resid 21 through 32 or resid 34...DC133 - 134133 - 134
4651LEULEULEULEU(chain 'D' and (resid 21 through 32 or resid 34...DC138138
4661VALVALLEULEU(chain 'D' and (resid 21 through 32 or resid 34...DC141 - 144141 - 144
4671GLYGLYSERSER(chain 'D' and (resid 21 through 32 or resid 34...DC146 - 157146 - 157
4681PROPROTRPTRP(chain 'D' and (resid 21 through 32 or resid 34...DC163 - 164163 - 164
4691TRPTRPTRPTRP(chain 'D' and (resid 21 through 32 or resid 34...DC174174
4701ALAALALYSLYS(chain 'D' and (resid 21 through 32 or resid 34...DC176 - 228176 - 228
4711TYRTYRGLUGLU(chain 'D' and (resid 21 through 32 or resid 34...DC231 - 242231 - 242
4721ALAALAGLUGLU(chain 'D' and (resid 21 through 32 or resid 34...DC246 - 248246 - 248
4731ARGARGGLNGLN(chain 'D' and (resid 21 through 32 or resid 34...DC250 - 260250 - 260
4741LEULEULEULEU(chain 'D' and (resid 21 through 32 or resid 34...DC264264
4751ARGARGARGARG(chain 'D' and (resid 21 through 32 or resid 34...DC267267
4761ALAALAGLYGLY(chain 'D' and (resid 21 through 32 or resid 34...DC269 - 278269 - 278
1772DADADTDTchain 'E'EE7 - 217 - 21
2782DADADTDTchain 'G'GG7 - 217 - 21

NCS ensembles :
ID
1
2

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Components

#1: Protein
CRISPR-associated endonuclease Cas1 2


Mass: 35999.703 Da / Num. of mol.: 4
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
#2: DNA chain DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*GP*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 7089.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')


Mass: 6938.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY
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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium chloride, 0.1M calcium chloride, 20% PEG 4000, 0.05M Tris-HCl
PH range: 8.0-9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97910,0.97937,0.96414
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.979371
30.964141
ReflectionResolution: 3.1→50 Å / Num. obs: 33449 / % possible obs: 99.6 % / Redundancy: 18.1 % / Biso Wilson estimate: 115.47 Å2 / Rsym value: 0.13 / Net I/σ(I): 19
Reflection shellResolution: 3.1→3.15 Å / Num. unique obs: 1633 / Rsym value: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 3.11→19.89 Å / SU ML: 0.5937 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.6333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2792 1698 5.1 %
Rwork0.2392 31596 -
obs0.2413 33294 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.34 Å2
Refinement stepCycle: LAST / Resolution: 3.11→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8107 1067 0 0 9174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00699476
X-RAY DIFFRACTIONf_angle_d0.953613076
X-RAY DIFFRACTIONf_chiral_restr0.06051440
X-RAY DIFFRACTIONf_plane_restr0.00561526
X-RAY DIFFRACTIONf_dihedral_angle_d23.28263384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.20.45071310.43272333X-RAY DIFFRACTION90.96
3.2-3.30.43221240.40012623X-RAY DIFFRACTION99.64
3.3-3.420.37581450.35862641X-RAY DIFFRACTION99.96
3.42-3.550.36641640.32562569X-RAY DIFFRACTION99.93
3.55-3.710.34721460.29882635X-RAY DIFFRACTION100
3.71-3.910.28651370.25672638X-RAY DIFFRACTION99.96
3.91-4.150.28011660.23022603X-RAY DIFFRACTION99.93
4.15-4.470.23371360.21462660X-RAY DIFFRACTION99.96
4.47-4.910.25631280.20112680X-RAY DIFFRACTION100
4.91-5.610.27721320.21862696X-RAY DIFFRACTION100
5.61-7.010.29391550.24212695X-RAY DIFFRACTION100
7.01-19.890.22711340.20282823X-RAY DIFFRACTION99.56

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