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

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Basic information

Entry
Database: PDB / ID: 3qrr
TitleStructure of Thermus Thermophilus Cse3 bound to an RNA representing a product 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*(23G))-3')
KeywordsRNA BINDING PROTEIN/RNA / protein-RNA complex / RAMP domain / 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 / RNA (> 10) / CRISPR-associated endoribonuclease Cse3
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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

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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*GP*CP*GP*UP*GP*UP*GP*GP*GP*(23G))-3')


Theoretical massNumber of molelcules
Total (without water)35,8602
Polymers35,8602
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*(23G))-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*(23G))-3')


Theoretical massNumber of molelcules
Total (without water)71,7204
Polymers71,7204
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area6820 Å2
ΔGint-32 kcal/mol
Surface area25360 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*(23G))-3')


Theoretical massNumber of molelcules
Total (without water)35,8602
Polymers35,8602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area1530 Å2
ΔGint-13 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.170, 68.747, 155.840
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: RNA chain RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*(23G))-3')


Mass: 5857.448 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: 47.02 %
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: ALS / Beamline: 12.3.1 / Wavelength: 1.11588 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 11, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 3.099→46.111 Å / Num. all: 6367 / Num. obs: 6268 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.099→3.179 Å / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.5.0110phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.099→46.111 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.818 / WRfactor Rfree: 0.2688 / WRfactor Rwork: 0.2146 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8387 / SU B: 39.225 / SU ML: 0.348 / SU R Cruickshank DPI: 0.4553 / SU Rfree: 0.552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3003 288 4.6 %RANDOM
Rwork0.2454 ---
obs0.2479 5979 98.41 %-
all-6076 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.16 Å2 / Biso mean: 55.434 Å2 / Biso min: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---1.26 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 3.099→46.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 386 0 0 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222098
X-RAY DIFFRACTIONr_angle_refined_deg0.6572.2262928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2835202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87221.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39515293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8831525
X-RAY DIFFRACTIONr_chiral_restr0.0340.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211455
X-RAY DIFFRACTIONr_mcbond_it0.1421.51021
X-RAY DIFFRACTIONr_mcangle_it0.25921639
X-RAY DIFFRACTIONr_scbond_it0.2331077
X-RAY DIFFRACTIONr_scangle_it0.394.51289
LS refinement shellResolution: 3.099→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 18 -
Rwork0.315 421 -
all-439 -
obs--98.87 %
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)
13.84751.20450.4273.04220.87541.91670.0915-0.07950.00690.1642-0.10350.0043-0.0783-0.05040.0120.05440.0323-0.01250.1570.00550.3369-20.184-12.526-26.944
22.4125-0.0423.13720.0449-0.10154.38040.0137-0.1858-0.0636-0.03690.1552-0.03110.3189-0.241-0.16890.36970.0101-0.1970.6031-0.01330.37-1.883-14.8430.678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 219
2X-RAY DIFFRACTION2B4 - 21

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