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- PDB-1t5i: Crystal structure of the C-terminal domain of UAP56 -

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Basic information

Entry
Database: PDB / ID: 1t5i
TitleCrystal structure of the C-terminal domain of UAP56
ComponentsC_TERMINAL DOMAIN OF A PROBABLE ATP-DEPENDENT RNA HELICASE
KeywordsPRE-MRNA PROCESSING PROTEIN / RecA-like fold
Function / homology
Function and homology information


transcription export complex / U6 snRNP / RNA secondary structure unwinding / ATP-dependent activity, acting on RNA / U4 snRNA binding / mRNA 3'-end processing / RNA export from nucleus / ATP-dependent protein binding / U4 snRNP / Transport of Mature mRNA derived from an Intron-Containing Transcript ...transcription export complex / U6 snRNP / RNA secondary structure unwinding / ATP-dependent activity, acting on RNA / U4 snRNA binding / mRNA 3'-end processing / RNA export from nucleus / ATP-dependent protein binding / U4 snRNP / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / spliceosomal complex assembly / U6 snRNA binding / RHOBTB2 GTPase cycle / mRNA export from nucleus / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / nuclear speck / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal ...RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Spliceosome RNA helicase DDX39B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsZhao, R. / Green, M.R. / Shen, J.
CitationJournal: Structure / Year: 2004
Title: Crystal structure of UAP56, a "DEXD/H-box" protein involved in pre-mRNA splicing and mRNA export
Authors: Zhao, R. / Shen, J. / Green, M.R. / Macmorris, M. / Blumenthal, T.
History
DepositionMay 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C_TERMINAL DOMAIN OF A PROBABLE ATP-DEPENDENT RNA HELICASE


Theoretical massNumber of molelcules
Total (without water)20,0421
Polymers20,0421
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.582, 33.582, 119.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein C_TERMINAL DOMAIN OF A PROBABLE ATP-DEPENDENT RNA HELICASE / U2AF65 associated protein 56 / UAP56


Mass: 20041.703 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 259-428)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAT1 / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q13838
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.68 Å3/Da / Density % sol: 26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MOPS, NaCl, Sodium Phosphate, Potassium Phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.97934, 0.97949, 0.96411
SYNCHROTRONAPS 19-ID21.0332
Detector
IDDetectorDate
1CCDOct 10, 2003
2CCDOct 10, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979491
30.964111
41.03321
ReflectionResolution: 1.9→30 Å / Num. all: 10414 / Num. obs: 9977 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.8 / Num. unique all: 750 / % possible all: 72

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Isotropic thermal model: isotropic / Cross valid method: Rfree / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 690 7 %random
Rwork0.2235 ---
all-10363 --
obs-9595 92.6 %-
Solvent computationBsol: 43.3131 Å2 / ksol: 0.383494 e/Å3
Displacement parametersBiso mean: 28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.307 Å0.2499 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 0 87 1398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.343
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_dihedral_angle_d22.37
X-RAY DIFFRACTIONc_mcbond_it2.186
X-RAY DIFFRACTIONc_mcangle_it3.527
X-RAY DIFFRACTIONc_scbond_it3.588
X-RAY DIFFRACTIONc_scangle_it5.683
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2485 45 7 %
Rwork0.2873 625 -
obs-463 64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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