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- PDB-1s29: La autoantigen N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1s29
TitleLa autoantigen N-terminal domain
ComponentsLa protein
KeywordsRNA BINDING PROTEIN / winged helix-turn-helix / autoantigen / RNA-binding
Function / homology
Function and homology information


maturation of 5S rRNA / RNA processing / ribosome biogenesis / ribonucleoprotein complex / mRNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Lupus La protein / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Lupus La protein / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA binding protein La-like protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsDong, G. / Chakshusmathi, G. / Wolin, S.L. / Reinisch, K.M.
CitationJournal: Embo J. / Year: 2004
Title: Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch.
Authors: Dong, G. / Chakshusmathi, G. / Wolin, S.L. / Reinisch, K.M.
History
DepositionJan 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: La protein


Theoretical massNumber of molelcules
Total (without water)10,6521
Polymers10,6521
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.926, 53.912, 53.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein La protein


Mass: 10651.736 Da / Num. of mol.: 1 / Fragment: N-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NIH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.14 % / Description: Friedel pairs were used.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3500, GLYCEROL, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1reservoirpH7.5
25 %(v/v)glycerol1reservoir
332-36 %(w/v)PEG35001reservoir
410 mMdithiothreitol1drop
510-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Aug 15, 2003
RadiationMonochromator: double-crystal monochromator Si(111), beam focused by a toroidal mirror
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 24632 / Num. obs: 24632 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 41
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 21 / % possible all: 95.7
Reflection
*PLUS
Num. obs: 24672 / Redundancy: 7 %
Reflection shell
*PLUS
Highest resolution: 1.59 Å / Lowest resolution: 1.65 Å / % possible obs: 95.7 % / Redundancy: 4.1 % / Num. unique obs: 2382 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.45 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 616074.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1347 10.3 %RANDOM
Rwork0.232 ---
all0.235 14446 --
obs0.232 13099 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.7058 Å2 / ksol: 0.548385 e/Å3
Displacement parametersBiso mean: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.61 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 0 100 837
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 223 10.7 %
Rwork0.227 1861 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00526
X-RAY DIFFRACTIONc_angle_deg1.169
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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