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

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Basic information

Entry
Database: PDB / ID: 3qrp
TitleStructure of Thermus Thermophilus Cse3 bound to an RNA representing a product mimic complex
Components
  • Putative uncharacterized protein TTHB192
  • RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*(PGP))-3')
  • RNA (5'-R(P*(U5P)P*GP*UP*GP*GP*GP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / RAMP domain / protein-RNA complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


endonuclease activity / defense response to virus / 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
RNA / CRISPR-associated endoribonuclease Cse3
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.352 Å
AuthorsSchellenberg, M.J. / Gesner, E.M. / 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Putative uncharacterized protein TTHB192
B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*(PGP))-3')
C: RNA (5'-R(P*(U5P)P*GP*UP*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2794
Polymers35,1833
Non-polymers961
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-38 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.057, 72.405, 100.225
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: RNA chain RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*(PGP))-3')


Mass: 2886.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized RNA
#3: RNA chain RNA (5'-R(P*(U5P)P*GP*UP*GP*GP*GP*G)-3')


Mass: 2293.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized RNA
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.91 Å3/Da / Density % sol: 35.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 8000, 100mM KCl, 5mM MgSO4, 1mM spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 27, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.352→34.752 Å / Num. all: 11772 / Num. obs: 11249 / % possible obs: 95.52 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.352→2.43 Å / % possible all: 75.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.55 Å32.99 Å
Translation2.55 Å32.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.352→34.752 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.1958 / WRfactor Rwork: 0.1778 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.881 / SU B: 9.947 / SU ML: 0.134 / SU R Cruickshank DPI: 0.5048 / SU Rfree: 0.2155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.463 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 534 4.7 %RANDOM
Rwork0.1753 ---
obs0.1774 11249 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.31 Å2 / Biso mean: 24.391 Å2 / Biso min: 7.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---0.47 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.352→34.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 345 5 152 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222133
X-RAY DIFFRACTIONr_angle_refined_deg1.5182.22963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2735213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4421.51979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63515311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.091525
X-RAY DIFFRACTIONr_chiral_restr0.1060.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021498
X-RAY DIFFRACTIONr_nbd_refined0.2270.2842
X-RAY DIFFRACTIONr_nbtor_refined0.310.21365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.215
X-RAY DIFFRACTIONr_mcbond_it1.6811.51104
X-RAY DIFFRACTIONr_mcangle_it2.22821715
X-RAY DIFFRACTIONr_scbond_it3.74431282
X-RAY DIFFRACTIONr_scangle_it4.5934.51248
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 30 -
Rwork0.185 590 -
all-620 -
obs--72.26 %
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)
10.27970.0215-0.06250.3220.08980.40840.01090.0078-0.01720.018-0.01370.0268-0.01260.00290.0028-0.0288-0.00620.0065-0.0263-0.0025-0.0172-8.481-15.57414.362
20.9221-0.0211-0.45130.68420.40430.87720.0170.0241-0.00050.1666-0.03820.08810.0515-0.0310.02110.0308-0.01420.0089-0.03980.0045-0.0381-11.93-16.332.315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 219
2X-RAY DIFFRACTION2B4 - 21

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