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- PDB-1key: Crystal Structure of Mouse Testis/Brain RNA-binding Protein (TB-RBP) -

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Basic information

Entry
Database: PDB / ID: 1key
TitleCrystal Structure of Mouse Testis/Brain RNA-binding Protein (TB-RBP)
Componentstranslin
KeywordsRNA BINDING PROTEIN / RNA-binding protein / tetramer/octamer assembly / apoTB-RBP
Function / homology
Function and homology information


Small interfering RNA (siRNA) biogenesis / RNA endonuclease activity / single-stranded DNA binding / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / mRNA binding / protein-containing complex binding / endoplasmic reticulum / RNA binding / nucleoplasm ...Small interfering RNA (siRNA) biogenesis / RNA endonuclease activity / single-stranded DNA binding / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / mRNA binding / protein-containing complex binding / endoplasmic reticulum / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Translin; domain 2 / Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsPascal, J.M. / Hart, P.J. / Hecht, N.B. / Robertus, J.D.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of TB-RBP, a Novel RNA-binding and Regulating Protein
Authors: Pascal, J.M. / Hart, P.J. / Hecht, N.B. / Robertus, J.D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Mouse testis-brain RNA-binding protein (TB-RBP): expression, purification, and crystal X-ray diffraction
Authors: Pascal, J.M. / Chennathukuzhi, V.M. / Hecht, N.B. / Robertus, J.D.
History
DepositionNov 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). Applying the 2-fold crystallographic operator (along the c axis) to the tetramer AU will create a molecular octamer of TB-RBP discussed in the corresponding paper. The actual biological state of the molecule is still under question.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: translin
B: translin
C: translin
D: translin


Theoretical massNumber of molelcules
Total (without water)107,7114
Polymers107,7114
Non-polymers00
Water1,47782
1
A: translin
B: translin
C: translin
D: translin

A: translin
B: translin
C: translin
D: translin


Theoretical massNumber of molelcules
Total (without water)215,4218
Polymers215,4218
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.246, 135.457, 91.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe asymmetric unit contains four TB-RBP monomers, each interacting to form a tetramer. A second tetramer produced by two-fold rotation of the crystallographic c axis forms an octamer of TB-RBP in the crystal.

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Components

#1: Protein
translin / / TB-RBP


Mass: 26927.654 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62348
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Ammomium Sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Pascal, J.M., (2001) Acta Cryst., D57, 1692.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X12B20.9794
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJun 15, 2000
ADSC QUANTUM 42CCDOct 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97941
ReflectionResolution: 2.65→50 Å / Num. all: 34219 / Num. obs: 34219 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 193026 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
DMmodel building
CNS1refinement
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 1741 5% of data throughout refinement
Rwork0.247 --
all-35613 -
obs-34973 -
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6927 0 0 82 7009
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.071
X-RAY DIFFRACTIONc_improper_angle_d0.688
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d18.251
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.251
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.688

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