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- PDB-5dqu: Crystal Structure of Cas-DNA-10 complex -

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Basic information

Entry
Database: PDB / ID: 5dqu
TitleCrystal Structure of Cas-DNA-10 complex
Components
  • CRISPR-associated endonuclease Cas1
  • CRISPR-associated endoribonuclease Cas2
  • DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')
KeywordsHYDROLASE/DNA / protein-DNA complex / HYDROLASE-DNA complex
Function / homology
Function and homology information


CRISPR-cas system / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / maintenance of CRISPR repeat elements / defense response to virus / endonuclease activity / 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 / defense response to virus / endonuclease activity / 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 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 speciesEscherichia coli K12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsWang, J. / Li, J. / Zhao, H. / Sheng, G. / Wang, M. / Yin, M. / Wang, Y.
CitationJournal: Cell / Year: 2015
Title: Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems.
Authors: Wang, J. / Li, J. / Zhao, H. / Sheng, G. / Wang, M. / Yin, M. / Wang, Y.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
E: CRISPR-associated endoribonuclease Cas2
D: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
F: CRISPR-associated endoribonuclease Cas2
B: CRISPR-associated endonuclease Cas1
H: DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*TP*TP*TP*T)-3')
I: DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*TP*TP*TP*T)-3')
J: DNA (5'-D(P*TP*TP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')
G: DNA (5'-D(P*TP*TP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)170,43510
Polymers170,43510
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23330 Å2
ΔGint-146 kcal/mol
Surface area58200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.095, 195.775, 194.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22C
13A
23B
14E
24F
15D
25C
16D
26B
17C
27B
18H
28I
19J
29G

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALPROPROAA15 - 28015 - 280
21VALVALPROPRODC15 - 28015 - 280
12VALVALPROPROAA15 - 27915 - 279
22VALVALPROPROCD15 - 27915 - 279
13VALVALILEILEAA15 - 27715 - 277
23VALVALILEILEBF15 - 27715 - 277
14SERSERLEULEUEB2 - 922 - 92
24SERSERLEULEUFE2 - 922 - 92
15VALVALALAALADC15 - 28115 - 281
25VALVALALAALACD15 - 28115 - 281
16VALVALILEILEDC15 - 27715 - 277
26VALVALILEILEBF15 - 27715 - 277
17TRPTRPILEILECD3 - 2773 - 277
27TRPTRPILEILEBF3 - 2773 - 277
18DGDGDTDTHG1 - 151 - 15
28DGDGDTDTIH601 - 6151 - 15
19DTDTDCDCJI5 - 161 - 12
29DTDTDCDCGJ9 - 201 - 12

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: 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 K12 (bacteria) / Strain: K12 / Gene: ygbT, cas1, b2755, JW2725 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q46896, Hydrolases; Acting on ester bonds
#2: Protein CRISPR-associated endoribonuclease Cas2


Mass: 10527.212 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: ygbF, cas2, b2754, JW5438 / Production host: Escherichia coli (E. coli)
References: UniProt: P45956, Hydrolases; Acting on ester bonds
#3: DNA chain DNA (5'-D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*TP*TP*TP*T)-3')


Mass: 4605.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA-10-1 / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(P*TP*TP*GP*CP*AP*TP*CP*GP*AP*CP*TP*C)-3')


Mass: 3613.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA-10-2 / Source: (synth.) Escherichia coli (E. coli)

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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: 4.31 Å3/Da / Density % sol: 71.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 8% PEG8000,100mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2014 / Details: Mono-chromator and mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 17232 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.067 / Rrim(I) all: 0.169 / Χ2: 0.913 / Net I/av σ(I): 9.338 / Net I/σ(I): 6.4 / Num. measured all: 106617
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.5-4.666.10.68816570.820.30.7520.904100
4.66-4.856.30.51716930.8630.220.5620.93799.9
4.85-5.076.30.49916990.8780.2120.5430.914100
5.07-5.336.30.4116800.9030.1750.4470.92100
5.33-5.6760.33517050.9210.1470.3660.92199.9
5.67-6.115.90.29617020.9220.1310.3240.936100
6.11-6.726.50.23317230.950.0980.2530.905100
6.72-7.696.50.16517340.9770.0690.1790.917100
7.69-9.675.90.12317610.9790.0550.1350.86999.9
9.67-5060.12318780.9590.0540.1350.90899.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6I

4p6i


Resolution: 4.5→50 Å / Cor.coef. Fo:Fc: 0.805 / Cor.coef. Fo:Fc free: 0.781 / SU B: 70.998 / SU ML: 0.852 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 852 5 %RANDOM
Rwork0.2646 ---
obs0.2657 16155 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 176.5 Å2 / Biso mean: 64.582 Å2 / Biso min: 16.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å20 Å2-0 Å2
2--0.11 Å20 Å2
3---2.24 Å2
Refinement stepCycle: final / Resolution: 4.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9578 1094 0 0 10672
Num. residues----1301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01810942
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210314
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.87615067
X-RAY DIFFRACTIONr_angle_other_deg1.511323641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49851239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15322.353391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.905151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6541596
X-RAY DIFFRACTIONr_chiral_restr0.0750.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111528
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022412
X-RAY DIFFRACTIONr_mcbond_it2.8946.3174995
X-RAY DIFFRACTIONr_mcbond_other2.8916.3174994
X-RAY DIFFRACTIONr_mcangle_it5.159.4696221
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A152170.1
12D152170.1
21A117280.22
22C117280.22
31A116740.22
32B116740.22
41E52460.07
42F52460.07
51D117760.22
52C117760.22
61D116200.22
62B116200.22
71C160880.09
72B160880.09
81H12440.01
82I12440.01
91J9490.01
92G9490.01
LS refinement shellResolution: 4.5→4.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 37 -
Rwork0.303 956 -
all-993 -
obs--80.21 %

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