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- PDB-1jri: The Crystal Structure of an Sm-like Archaeal Protein with Two Hep... -

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Basic information

Entry
Database: PDB / ID: 1jri
TitleThe Crystal Structure of an Sm-like Archaeal Protein with Two Heptamers in the Asymmetric Unit.
ComponentsSm-like Archaeal Protein 1 (SmAP1)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / heptameric / 35-stranded beta toroid
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: 2.8 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
DepositionAug 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 21, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: refine / struct_biol ...refine / struct_biol / struct_ref_seq_dif / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details ..._refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sm-like Archaeal Protein 1 (SmAP1)
B: Sm-like Archaeal Protein 1 (SmAP1)
C: Sm-like Archaeal Protein 1 (SmAP1)
D: Sm-like Archaeal Protein 1 (SmAP1)
E: Sm-like Archaeal Protein 1 (SmAP1)
F: Sm-like Archaeal Protein 1 (SmAP1)
G: Sm-like Archaeal Protein 1 (SmAP1)
H: Sm-like Archaeal Protein 1 (SmAP1)
I: Sm-like Archaeal Protein 1 (SmAP1)
J: Sm-like Archaeal Protein 1 (SmAP1)
K: Sm-like Archaeal Protein 1 (SmAP1)
L: Sm-like Archaeal Protein 1 (SmAP1)
M: Sm-like Archaeal Protein 1 (SmAP1)
N: Sm-like Archaeal Protein 1 (SmAP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,95430
Polymers133,04114
Non-polymers91316
Water1,54986
1
A: Sm-like Archaeal Protein 1 (SmAP1)
B: Sm-like Archaeal Protein 1 (SmAP1)
C: Sm-like Archaeal Protein 1 (SmAP1)
D: Sm-like Archaeal Protein 1 (SmAP1)
E: Sm-like Archaeal Protein 1 (SmAP1)
F: Sm-like Archaeal Protein 1 (SmAP1)
G: Sm-like Archaeal Protein 1 (SmAP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,90214
Polymers66,5207
Non-polymers3817
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-53 kcal/mol
Surface area24810 Å2
MethodPISA
2
H: Sm-like Archaeal Protein 1 (SmAP1)
I: Sm-like Archaeal Protein 1 (SmAP1)
J: Sm-like Archaeal Protein 1 (SmAP1)
K: Sm-like Archaeal Protein 1 (SmAP1)
L: Sm-like Archaeal Protein 1 (SmAP1)
M: Sm-like Archaeal Protein 1 (SmAP1)
N: Sm-like Archaeal Protein 1 (SmAP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,05216
Polymers66,5207
Non-polymers5329
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-37 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.371, 114.698, 238.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit of the P212121 lattice contains two copies of the biologically significant assembly (a heptamer), the tangential rings being roughly coplanar (~15 degrees deviation).

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Components

#1: Protein
Sm-like Archaeal Protein 1 (SmAP1) / PUTATIVE SNRNP SM-LIKE PROTEIN


Mass: 9502.921 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: Mth0649 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O26745
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 292.8 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 10% v/v isopropanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 19.8K
Crystal grow
*PLUS
pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
142 mg/mlprotein1drop
210 mMTris1droppH7.8
35 mMEDTA1droppH8.0
40.1 M1dropNaCl
50.1 MTris1reservoirpH8.50
610 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2001 / Details: fine-focussing mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 28487 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 19.3
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2645 / % possible all: 92.5
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 329838
Reflection shell
*PLUS
% possible obs: 92.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JBM

1jbm


Resolution: 2.8→14.95 Å
Isotropic thermal model: restrained isotropic temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1319 -RANDOM 5% of data over entire data range (100-2.8 A)
Rwork0.199 ---
all-26759 --
obs-26759 94.9 %-
Displacement parametersBiso mean: 52.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.8→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8085 0 55 86 8226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.375 --
Rwork0.28 --
obs-3936 0.901 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.375 / Rfactor Rwork: 0.28

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