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- PDB-4qqy: Crystal structure of T. fusca Cas3-ADP -

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Basic information

Entry
Database: PDB / ID: 4qqy
TitleCrystal structure of T. fusca Cas3-ADP
Components
  • CRISPR-associated helicase, Cas3 family
  • HD nuclease
KeywordsHydrolase/DNA / RISPR / 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 nuclease/helicase Cas3, C-terminal / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / 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 nuclease/helicase Cas3, C-terminal / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / : / DNA / DNA (> 10) / CRISPR-associated helicase, Cas3 family
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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: HD nuclease
C: CRISPR-associated helicase, Cas3 family
D: HD nuclease
E: CRISPR-associated helicase, Cas3 family
F: HD nuclease
G: CRISPR-associated helicase, Cas3 family
H: HD nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,85220
Polymers439,6978
Non-polymers2,15612
Water00
1
A: CRISPR-associated helicase, Cas3 family
B: HD nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4635
Polymers109,9242
Non-polymers5393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CRISPR-associated helicase, Cas3 family
D: HD nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4635
Polymers109,9242
Non-polymers5393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: CRISPR-associated helicase, Cas3 family
F: HD nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4635
Polymers109,9242
Non-polymers5393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: CRISPR-associated helicase, Cas3 family
H: HD nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4635
Polymers109,9242
Non-polymers5393
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: CRISPR-associated helicase, Cas3 family
B: HD nuclease
C: CRISPR-associated helicase, Cas3 family
D: HD nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,92610
Polymers219,8484
Non-polymers1,0786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-94 kcal/mol
Surface area71990 Å2
MethodPISA
6
E: CRISPR-associated helicase, Cas3 family
F: HD nuclease
G: CRISPR-associated helicase, Cas3 family
H: HD nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,92610
Polymers219,8484
Non-polymers1,0786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-94 kcal/mol
Surface area71780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.206, 222.607, 124.847
Angle α, β, γ (deg.)90.000, 104.070, 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
HD nuclease


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: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.67 Å3/Da / Density % sol: 53.99 %
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 3151CCDApr 5, 2013
ADSC QUANTUM 2102CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.12→50 Å / Num. all: 76497 / Num. obs: 81891 / % possible obs: 99.21 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.3
Reflection shellResolution: 3.12→3.27 Å / % possible all: 98.3

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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: 3.12→47.836 Å / FOM work R set: 0.8197 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1624 2.02 %random
Rwork0.17 ---
obs0.1713 80395 98.2 %-
all-80395 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.55 Å2 / Biso mean: 76.26 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.12→47.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27922 788 116 0 28826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01529664
X-RAY DIFFRACTIONf_angle_d1.47440665
X-RAY DIFFRACTIONf_chiral_restr0.0844553
X-RAY DIFFRACTIONf_plane_restr0.0065126
X-RAY DIFFRACTIONf_dihedral_angle_d18.27610860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.12-3.21180.33511360.24246617675399
3.2118-3.31540.35051360.23966583671999
3.3154-3.43390.32191360.2176610674699
3.4339-3.57140.30271360.20196596673299
3.5714-3.73380.24251360.17686586672299
3.7338-3.93060.25211370.17096635677299
3.9306-4.17670.25931360.15766587672399
4.1767-4.4990.20831340.14396530666498
4.499-4.95130.18231350.13836566670198
4.9513-5.66680.22191350.16046535667097
5.6668-7.13580.23691330.1846485661897
7.1358-47.84160.17351340.15066441657595

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