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- PDB-3sk9: Crystal structure of the Thermus thermophilus cas3 HD domain -

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Basic information

Entry
Database: PDB / ID: 3sk9
TitleCrystal structure of the Thermus thermophilus cas3 HD domain
ComponentsPutative uncharacterized protein TTHB187
KeywordsHYDROLASE / CRISPR / CAS / HD domain / nuclease
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA helicase activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Cas3, C-terminal / 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. ...Cas3, C-terminal / 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 / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CRISPR-associated endonuclease/helicase Cas3
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.8 Å
AuthorsBailey, S. / Mulepati, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Biochemical Analysis of Nuclease Domain of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Protein 3 (Cas3).
Authors: Mulepati, S. / Bailey, S.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Data collection
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Oct 19, 2011Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHB187


Theoretical massNumber of molelcules
Total (without water)29,7231
Polymers29,7231
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.638, 48.638, 206.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Putative uncharacterized protein TTHB187


Mass: 29722.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHB187 / Plasmid: pHAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): T7EXPRESS / References: UniProt: Q53VY2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PEG 300, pH 4.2, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.798→39.691 Å / Num. all: 23815 / Num. obs: 23815 / % possible obs: 99.4 % / Redundancy: 11.7 % / Rsym value: 0.061 / Net I/σ(I): 22.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.910.70.4951.63479232510.49596.4
1.9-2.0111.50.3262.33727832450.326100
2.01-2.1511.70.1864.13558530350.186100
2.15-2.3212.60.1325.43578428500.132100
2.32-2.5412.30.0987.63243926410.098100
2.54-2.8412.40.0779.42987024140.077100
2.84-3.2812.40.0611.92652921420.06100
3.28-4.02110.044152039418470.04499.8
4.02-5.6911.60.03817.91714314780.038100
5.69-39.546100.0320.791399120.0399.7

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Phasing

PhasingMethod: MIRAS
Phasing dmFOM : 0.72 / FOM acentric: 0.73 / FOM centric: 0.72 / Reflection: 733 / Reflection acentric: 397 / Reflection centric: 336
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-19.9870.750.750.76443220223
4.5-7.10.680.70.65290177113
3.6-4.5
3.1-3.6
2.7-3.1
2.5-2.7
Phasing MIRResolution: 2.5→20 Å / FOM: 0.51 / Reflection: 8978
Phasing MIR der
IDDer set-ID
11
21
31
41
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1160Pt0.46290.20230.8830.3233
1260Pt0.44560.52640.97210.2253
1346.6837Pt0.40170.23830.8910.2109
149.2574Pt0.41680.51720.85940.0816
2134.0627Os0.560.53030.02520.3251
Phasing MIR shell
Resolution (Å)FOMReflection
8.52-200.74536
5.54-8.520.67785
4.38-5.540.55969
3.74-4.380.491139
3.31-3.740.491255
3-3.310.481343
2.77-30.451450
2.58-2.770.41501

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
SOLVE2.13phasing
RESOLVE2.15phasing
PHENIX1.6_288refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MIRAS / Resolution: 1.8→39.691 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.9003 / SU ML: 0.19 / σ(F): 0.41 / Phase error: 17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 2195 5.03 %
Rwork0.1669 --
obs0.1683 -99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.429 Å2 / ksol: 0.416 e/Å3
Displacement parametersBiso max: 104.6 Å2 / Biso mean: 32.6815 Å2 / Biso min: 14.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.8461 Å2-0 Å20 Å2
2---1.8461 Å2-0 Å2
3---3.6922 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 0 105 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161887
X-RAY DIFFRACTIONf_angle_d1.4252565
X-RAY DIFFRACTIONf_chiral_restr0.097267
X-RAY DIFFRACTIONf_plane_restr0.008336
X-RAY DIFFRACTIONf_dihedral_angle_d15.082687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83910.24191060.212569267599
1.8391-1.88190.21711480.200725892737100
1.8819-1.9290.24441170.19626182735100
1.929-1.98110.23281350.181425892724100
1.9811-2.03940.23571650.162225902755100
2.0394-2.10530.19671330.15962569270299
2.1053-2.18050.17221470.152525712718100
2.1805-2.26780.22471240.161326132737100
2.2678-2.3710.18871130.163426412754100
2.371-2.4960.21831630.159625482711100
2.496-2.65230.19361700.156525952765100
2.6523-2.85710.16151650.154725752740100
2.8571-3.14450.18421250.166125762701100
3.1445-3.59920.19281370.160725942731100
3.5992-4.53360.16291250.15226072732100
4.5336-39.70020.21751220.1826192741100
Refinement TLS params.Method: refined / Origin x: 27.4364 Å / Origin y: 40.1666 Å / Origin z: 16.4034 Å
111213212223313233
T0.1008 Å2-0.0015 Å2-0.0114 Å2-0.0937 Å20.0033 Å2--0.0959 Å2
L0.7418 °20.1495 °20.0314 °2-0.2703 °20.1676 °2--0.4803 °2
S-0.004 Å °0.0387 Å °-0.0068 Å °0.0095 Å °-0.0082 Å °0.0133 Å °0.0138 Å °-0.0395 Å °0.0122 Å °
Refinement TLS groupSelection details: chain A

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