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- PDB-3qrq: Structure of Thermus Thermophilus Cse3 bound to an RNA representi... -

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Basic information

Entry
Database: PDB / ID: 3qrq
TitleStructure of Thermus Thermophilus Cse3 bound to an RNA representing a pre-cleavage complex
Components
  • Putative uncharacterized protein TTHB192
  • RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*GP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / protein-RNA complex / RAMP domain / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Crispr-associated protein; domain 1 / Crispr-associated protein; domain 2 / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA/RNA hybrid / DNA/RNA hybrid (> 10) / CRISPR-associated endoribonuclease Cse3
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.194 Å
AuthorsSchellenberg, M.J. / Gesner, E.G. / Garside, E.L. / MacMillan, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Recognition and maturation of effector RNAs in a CRISPR interference pathway.
Authors: Gesner, E.M. / Schellenberg, M.J. / Garside, E.L. / George, M.M. / Macmillan, A.M.
History
DepositionFeb 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 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 TTHB192
B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)36,1112
Polymers36,1112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein TTHB192
B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*GP*A)-3')

A: Putative uncharacterized protein TTHB192
B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)72,2224
Polymers72,2224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area7340 Å2
ΔGint-38 kcal/mol
Surface area25090 Å2
MethodPISA
3
A: Putative uncharacterized protein TTHB192

B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)36,1112
Polymers36,1112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area1800 Å2
ΔGint-14 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.500, 68.910, 158.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Putative uncharacterized protein TTHB192


Mass: 30002.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHB1192, TTHB192 / Plasmid: PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53WG9
#2: DNA/RNA hybrid RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*GP*A)-3')


Mass: 6108.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized RNA

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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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 100mM KOAc, 1mM spermidine, pH 7.5, vapour diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 1, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.194→45.884 Å / Num. all: 5874 / Num. obs: 5725 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.168 / Χ2: 1.004 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.194-3.313.70.4125141.023189.4
3.31-3.454.10.345230.976192.1
3.45-3.64.10.2765630.94197.4
3.6-3.794.20.1985560.899198.1
3.79-4.0350.1825790.952198.5
4.03-4.3411.40.2075771.0031100
4.34-4.7811.50.1725781.0271100
4.78-5.4711.30.1675971.0061100
5.47-6.8911.10.1885961.0261100
6.89-45.88410.30.0726421.031199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å45.88 Å
Translation3.5 Å45.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.194→45.884 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.856 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 50.057 / SU ML: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.533 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 272 4.8 %RANDOM
Rwork0.2101 ---
obs0.2129 5724 97.41 %-
all-5586 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.87 Å2 / Biso mean: 46.96 Å2 / Biso min: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---2.18 Å20 Å2
3---2.48 Å2
Refinement stepCycle: LAST / Resolution: 3.194→45.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 404 0 0 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222118
X-RAY DIFFRACTIONr_angle_refined_deg1.0082.2352961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1785202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70421.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89315293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5971525
X-RAY DIFFRACTIONr_chiral_restr0.1270.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021467
X-RAY DIFFRACTIONr_nbd_refined0.1850.2810
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21345
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.216
X-RAY DIFFRACTIONr_mcbond_it0.2781.51051
X-RAY DIFFRACTIONr_mcangle_it0.50321639
X-RAY DIFFRACTIONr_scbond_it0.47531348
X-RAY DIFFRACTIONr_scangle_it0.9374.51322
LS refinement shellResolution: 3.194→3.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 17 -
Rwork0.28 361 -
all-378 -
obs--87.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23630.90710.36092.76150.9651.19110.1209-0.08640.02720.1095-0.11220.018-0.0115-0.0474-0.0087-0.04420.0071-0.02350.16-0.00690.25-20.184-12.526-26.944
20.49340.08431.12030.01440.19142.5438-0.47140.04860.2181-0.05030.3372-0.1510.21010.30180.13420.21980.056-0.27240.6028-0.06290.2759-1.883-14.8430.678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 219
2X-RAY DIFFRACTION2B4 - 21

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