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- PDB-4qqw: Crystal structure of T. fusca Cas3 -

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Basic information

Entry
Database: PDB / ID: 4qqw
TitleCrystal structure of T. fusca Cas3
Components
  • CRISPR-associated helicase, Cas3 family
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsHydrolase/DNA / CRISPR / Cas3 / helicase / Hydrolase-DNA complex
Function / homology
Function and homology information


defense response to virus / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Hypothetical protein af1432 - #30 / Cas3 C-terminal domain / Helicase Cas3, CRISPR-associated, core / Cas3, HD domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / : / Hypothetical protein af1432 ...Hypothetical protein af1432 - #30 / Cas3 C-terminal domain / Helicase Cas3, CRISPR-associated, core / Cas3, HD domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / : / Hypothetical protein af1432 / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Helicase, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / CRISPR-associated helicase, Cas3 family
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.664 Å
AuthorsKe, A. / Huo, Y. / Nam, K.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation.
Authors: Huo, Y. / Nam, K.H. / Ding, F. / Lee, H. / Wu, L. / Xiao, Y. / Farchione, M.D. / Zhou, S. / Rajashankar, K. / Kurinov, I. / Zhang, R. / Ke, A.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated helicase, Cas3 family
B: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: CRISPR-associated helicase, Cas3 family
D: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
E: CRISPR-associated helicase, Cas3 family
F: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
G: CRISPR-associated helicase, Cas3 family
H: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,14316
Polymers439,6978
Non-polymers4478
Water3,873215
1
A: CRISPR-associated helicase, Cas3 family
B: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0364
Polymers109,9242
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CRISPR-associated helicase, Cas3 family
D: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0364
Polymers109,9242
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: CRISPR-associated helicase, Cas3 family
F: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0364
Polymers109,9242
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: CRISPR-associated helicase, Cas3 family
H: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0364
Polymers109,9242
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: CRISPR-associated helicase, Cas3 family
B: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: CRISPR-associated helicase, Cas3 family
D: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,0728
Polymers219,8484
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-92 kcal/mol
Surface area73080 Å2
MethodPISA
6
E: CRISPR-associated helicase, Cas3 family
F: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
G: CRISPR-associated helicase, Cas3 family
H: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,0728
Polymers219,8484
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-86 kcal/mol
Surface area72550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.789, 218.542, 123.749
Angle α, β, γ (deg.)90.000, 105.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CRISPR-associated helicase, Cas3 family


Mass: 106210.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_1593 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q47PJ0
#2: DNA chain
DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3713.524 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, pH 6.5, and 5% 10% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 24-ID-C1
SYNCHROTRONCHESS A12
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 28, 2011
ADSC QUANTUM 2102CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 115323 / Num. obs: 115323 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.1
Reflection shellResolution: 2.65→2.7 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.9 / % possible all: 86.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.664→30.207 Å / FOM work R set: 0.8267 / SU ML: 0.34 / σ(F): 1.39 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1999 1.73 %RANDOM
Rwork0.1731 ---
obs0.174 115323 92.12 %-
all-115323 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.44 Å2 / Biso mean: 58.03 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.664→30.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28027 788 8 215 29038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01729655
X-RAY DIFFRACTIONf_angle_d1.4140637
X-RAY DIFFRACTIONf_chiral_restr0.0824557
X-RAY DIFFRACTIONf_plane_restr0.0065145
X-RAY DIFFRACTIONf_dihedral_angle_d16.65710856
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6636-2.73020.29311200.25696883700379
2.7302-2.8040.31751370.24097724786188
2.804-2.88640.30991390.2337863800290
2.8864-2.97950.26651400.22437932807290
2.9795-3.08590.28421430.22438103824692
3.0859-3.20930.30191450.22168215836094
3.2093-3.35520.27511480.20978380852895
3.3552-3.53190.26441470.20428367851495
3.5319-3.75280.22361490.17548441859096
3.7528-4.04190.22191470.15758298844595
4.0419-4.44750.20511490.14588463861296
4.4475-5.08840.17721470.13888362850995
5.0884-6.40080.20721450.16248230837594
6.4008-30.20890.1721430.13588063820690

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