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- PDB-3hib: Crystal structure of the second Sec63 domain of yeast Brr2 -

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Basic information

Entry
Database: PDB / ID: 3hib
TitleCrystal structure of the second Sec63 domain of yeast Brr2
ComponentsPre-mRNA-splicing helicase BRR2
KeywordsHYDROLASE / RNA helicase / ATP-binding / Helicase / mRNA processing / mRNA splicing / Nucleotide-binding / Nucleus / Spliceosome
Function / homology
Function and homology information


spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U5 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / nucleic acid binding / RNA helicase / ATP hydrolysis activity / ATP binding ...spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U5 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / nucleic acid binding / RNA helicase / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus
Similarity search - Function
Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / DEAD/DEAH box helicase ...Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-splicing helicase BRR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, L. / Xu, T. / Zhao, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2.
Authors: Zhang, L. / Xu, T. / Maeder, C. / Bud, L.O. / Shanks, J. / Nix, J. / Guthrie, C. / Pleiss, J.A. / Zhao, R.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-splicing helicase BRR2


Theoretical massNumber of molelcules
Total (without water)36,2791
Polymers36,2791
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.153, 75.678, 83.955
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 Pre-mRNA-splicing helicase BRR2 / Protein Snu246


Mass: 36278.668 Da / Num. of mol.: 1 / Fragment: Second Sec63 domain: UNP residues 1851-2163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRR2, RSS1, SNU246, SYGP-ORF66, YER172C / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90
References: UniProt: P32639, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.64 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Sodium citrate, 17% PEG 8000, 0.2M NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9790, 0.9789, 0.9640
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 4, 2008
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97891
30.9641
ReflectionResolution: 2→40 Å / Num. all: 45853 / Num. obs: 45853 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2377 / % possible all: 100

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Processing

Software
NameClassification
CrystalCleardata collection
SOLVEphasing
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing and refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4375 -random
Rwork0.246 ---
obs0.246 45120 98.4 %-
Displacement parametersBiso mean: 36.28 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 0 192 2674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.674

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