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- PDB-1i81: CRYSTAL STRUCTURE OF A HEPTAMERIC LSM PROTEIN FROM METHANOBACTERI... -

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Basic information

Entry
Database: PDB / ID: 1i81
TitleCRYSTAL STRUCTURE OF A HEPTAMERIC LSM PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
ComponentsPUTATIVE SNRNP SM-LIKE PROTEIN
KeywordsSTRUCTURAL GENOMICS / Curved anti-parallel beta sheet
Function / homology
Function and homology information


Sm-like protein family complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding
Similarity search - Function
snRNP Sm-like, putative, archaea / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...snRNP Sm-like, putative, archaea / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCollins, B.M. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M.G. / Mabbutt, B.C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of a heptameric Sm-like protein complex from archaea: implications for the structure and evolution of snRNPs.
Authors: Collins, B.M. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M. / Mabbutt, B.C.
History
DepositionMar 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE SNRNP SM-LIKE PROTEIN
B: PUTATIVE SNRNP SM-LIKE PROTEIN
C: PUTATIVE SNRNP SM-LIKE PROTEIN
D: PUTATIVE SNRNP SM-LIKE PROTEIN
E: PUTATIVE SNRNP SM-LIKE PROTEIN
F: PUTATIVE SNRNP SM-LIKE PROTEIN
G: PUTATIVE SNRNP SM-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)64,2917
Polymers64,2917
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-43 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.380, 71.940, 94.670
Angle α, β, γ (deg.)90.00, 93.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PUTATIVE SNRNP SM-LIKE PROTEIN


Mass: 9184.438 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: MT0649 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (AMERSHAM PHARMACIA BIOTECH) / References: UniProt: O26745
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris PEG3350 Lithium sulphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
216 %(v/v)PEG33501reservoir
30.25 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 1, 2000 / Details: Focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. all: 119267 / Num. obs: 119267 / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.7
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 35595 / % possible obs: 98.2 % / Num. measured all: 119267
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 85.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model constructed from 1B34

1b34


Resolution: 2→15 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.2571 2595 random
Rwork0.2176 --
all-34516 -
obs-34516 -
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4022 0 0 155 4177
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.257 / Rfactor Rwork: 0.218 / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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