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- PDB-1jbm: Heptameric crystal structure of Mth649, an Sm-like archaeal prote... -

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Basic information

Entry
Database: PDB / ID: 1jbm
TitleHeptameric crystal structure of Mth649, an Sm-like archaeal protein from Methanobacterium thermautotrophicum
ComponentsPUTATIVE SNRNP SM-LIKE PROTEIN
KeywordsSTRUCTURAL GENOMICS / ring-shaped homoheptamer / all beta-strand
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
ACETIC ACID / Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMura, C. / Eisenberg, D.
CitationJournal: Protein Sci. / Year: 2003
Title: The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs)
Authors: Mura, C. / Kozhukhovsky, A. / Gingery, M. / Phillips, M. / Eisenberg, D.
History
DepositionJun 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,00123
Polymers67,0187
Non-polymers98316
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-6 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.066, 54.077, 62.346
Angle α, β, γ (deg.)87.58, 72.86, 81.45
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is the homoheptameric ring found in the asymmetric unit (P1 cell). There are no additional symmetry transformations.

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Components

#1: Protein
PUTATIVE SNRNP SM-LIKE PROTEIN


Mass: 9573.998 Da / Num. of mol.: 7 / Fragment: full-length Sm protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: Mth0649 ORF / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O26745
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG-4000, acetate, citrate buffer, NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→90 Å / Num. all: 44472 / Num. obs: 44472 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.4
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.14 / % possible all: 67.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I8F

1i8f


Resolution: 1.85→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2161 -random
Rwork0.196 ---
all0.196 47481 --
obs0.196 43390 91.4 %-
Displacement parametersBiso mean: 29.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 44 293 4423
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.06
X-RAY DIFFRACTIONc_dihedral_angle_d26.22
X-RAY DIFFRACTIONc_improper_angle_d1.28
LS refinement shellResolution: 1.85→1.92 Å
RfactorNum. reflection% reflection
Rfree0.313 131 -
Rwork0.274 --
obs-2824 56.3 %

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