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- PDB-2czj: Crystal structure of the tRNA domain of tmRNA from Thermus thermo... -

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Basic information

Entry
Database: PDB / ID: 2czj
TitleCrystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8
Components
  • SsrA-binding protein
  • tmRNA (63-MER)
KeywordsRNA BINDING PROTEIN/RNA / SmpB / tmRNA / SsrA RNA / 10Sa RNA / tRNA / trans-translation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


trans-translation / rRNA binding / cytosol
Similarity search - Function
Small Protein B; Chain: A; / Small protein B / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / SsrA-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsBessho, Y. / Shibata, R. / Sekine, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
Authors: Bessho, Y. / Shibata, R. / Sekine, S. / Murayama, K. / Higashijima, K. / Hori-Takemoto, C. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJul 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SsrA-binding protein
C: SsrA-binding protein
E: SsrA-binding protein
G: SsrA-binding protein
B: tmRNA (63-MER)
D: tmRNA (63-MER)
F: tmRNA (63-MER)
H: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)137,8668
Polymers137,8668
Non-polymers00
Water00
1
A: SsrA-binding protein
B: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)34,4672
Polymers34,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-6 kcal/mol
Surface area16330 Å2
MethodPISA
2
C: SsrA-binding protein
D: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)34,4672
Polymers34,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-5 kcal/mol
Surface area16500 Å2
MethodPISA
3
E: SsrA-binding protein
F: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)34,4672
Polymers34,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-6 kcal/mol
Surface area16800 Å2
MethodPISA
4
G: SsrA-binding protein
H: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)34,4672
Polymers34,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-4 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.776, 67.957, 178.662
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SsrA-binding protein


Mass: 14177.479 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RR57
#2: RNA chain
tmRNA (63-MER)


Mass: 20289.061 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Total 63nt of RNA was generated by binding T7 trascript (41nt) and chemically synthesized RNA (22nt).

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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: 3.7 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2ammonium sulfate11
3ammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2004
RadiationMonochromator: double flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→48.76 Å / Num. obs: 40370 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.33 % / Rsym value: 0.075 / Net I/σ(I): 23.69
Reflection shellResolution: 3.01→3.11 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 3977 / Rsym value: 0.366 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P6V, 1WJX

1p6v

1wjx


Resolution: 3.01→48.76 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THIS CRYSTAL HAS A PSEUDO-MEROHEDRAL PERFECT TWINNING. THE TWINNING OPERATER IS (H,K,L) -> (H,-K,-L). THE R-FACTOR IS 0.255 AND THE R-FREE IS 0.320 WHEN THIS TWINING OPERATOR IS USED WITH TWIN_LSQ TARGET.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 3034 7.4 %RANDOM
Rwork0.255 ---
obs-39488 96.7 %-
Displacement parametersBiso mean: 94.2 Å2
Refinement stepCycle: LAST / Resolution: 3.01→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 5292 0 0 9224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree: 0.375 / Rfactor Rwork: 0.361 / Total num. of bins used: 8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top

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