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- PDB-1m5q: Crystal structure of a novel Sm-like archaeal protein from Pyroba... -

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Basic information

Entry
Database: PDB / ID: 1m5q
TitleCrystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum
Componentssmall nuclear ribonucleoprotein homolog
KeywordsTRANSLATION / OB-like fold / b-sheet toroid / 14-mer / cadmium-binding site
Function / homology
Function and homology information


sno(s)RNA-containing ribonucleoprotein complex / mRNA splicing, via spliceosome / viral nucleocapsid / RNA binding
Similarity search - Function
Like-Sm ribonucleoprotein, C-terminal domain / Lsm, C-terminal / Like-Sm ribonucleoprotein, C-terminal domain superfamily / Lsm C-terminal / Ataxin 2, SM domain / Ataxin 2 SM domain / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins ...Like-Sm ribonucleoprotein, C-terminal domain / Lsm, C-terminal / Like-Sm ribonucleoprotein, C-terminal domain superfamily / Lsm C-terminal / Ataxin 2, SM domain / Ataxin 2 SM domain / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / TATA-Binding Protein / LSM domain superfamily / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / Small nuclear ribonucleoprotein homolog (Sm-like)
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMura, C. / Phillips, M. / Kozhukhovsky, A. / Eisenberg, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure and assembly of an augmented Sm-like archaeal protein 14-mer
Authors: Mura, C. / Phillips, M. / Kozhukhovsky, A. / Eisenberg, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core
Authors: Mura, C. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.
History
DepositionJul 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 17, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: small nuclear ribonucleoprotein homolog
B: small nuclear ribonucleoprotein homolog
C: small nuclear ribonucleoprotein homolog
D: small nuclear ribonucleoprotein homolog
E: small nuclear ribonucleoprotein homolog
F: small nuclear ribonucleoprotein homolog
G: small nuclear ribonucleoprotein homolog
H: small nuclear ribonucleoprotein homolog
I: small nuclear ribonucleoprotein homolog
J: small nuclear ribonucleoprotein homolog
K: small nuclear ribonucleoprotein homolog
L: small nuclear ribonucleoprotein homolog
M: small nuclear ribonucleoprotein homolog
N: small nuclear ribonucleoprotein homolog
O: small nuclear ribonucleoprotein homolog
P: small nuclear ribonucleoprotein homolog
Q: small nuclear ribonucleoprotein homolog
R: small nuclear ribonucleoprotein homolog
S: small nuclear ribonucleoprotein homolog
T: small nuclear ribonucleoprotein homolog
U: small nuclear ribonucleoprotein homolog
V: small nuclear ribonucleoprotein homolog
W: small nuclear ribonucleoprotein homolog
X: small nuclear ribonucleoprotein homolog
Y: small nuclear ribonucleoprotein homolog
Z: small nuclear ribonucleoprotein homolog
1: small nuclear ribonucleoprotein homolog
2: small nuclear ribonucleoprotein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,48888
Polymers420,21928
Non-polymers5,26860
Water34,0121888
1
A: small nuclear ribonucleoprotein homolog
B: small nuclear ribonucleoprotein homolog
C: small nuclear ribonucleoprotein homolog
D: small nuclear ribonucleoprotein homolog
E: small nuclear ribonucleoprotein homolog
F: small nuclear ribonucleoprotein homolog
G: small nuclear ribonucleoprotein homolog
H: small nuclear ribonucleoprotein homolog
I: small nuclear ribonucleoprotein homolog
J: small nuclear ribonucleoprotein homolog
K: small nuclear ribonucleoprotein homolog
L: small nuclear ribonucleoprotein homolog
M: small nuclear ribonucleoprotein homolog
N: small nuclear ribonucleoprotein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,70243
Polymers210,11014
Non-polymers2,59329
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51460 Å2
ΔGint-311 kcal/mol
Surface area69680 Å2
MethodPISA
2
O: small nuclear ribonucleoprotein homolog
P: small nuclear ribonucleoprotein homolog
Q: small nuclear ribonucleoprotein homolog
R: small nuclear ribonucleoprotein homolog
S: small nuclear ribonucleoprotein homolog
T: small nuclear ribonucleoprotein homolog
U: small nuclear ribonucleoprotein homolog
V: small nuclear ribonucleoprotein homolog
W: small nuclear ribonucleoprotein homolog
X: small nuclear ribonucleoprotein homolog
Y: small nuclear ribonucleoprotein homolog
Z: small nuclear ribonucleoprotein homolog
1: small nuclear ribonucleoprotein homolog
2: small nuclear ribonucleoprotein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,78545
Polymers210,11014
Non-polymers2,67631
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51770 Å2
ΔGint-325 kcal/mol
Surface area69010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.322, 172.427, 148.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological assembly is most likely a 14-mer (out of 28 chains in the asymmetric unit), formed by chains A-->N and by chains O-->2.

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Components

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Protein , 1 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ12

#1: Protein ...
small nuclear ribonucleoprotein homolog / SmAP3 / Sm-like archaeal protein (SmAP3) / Sm-like protein


Mass: 15007.830 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: SmAP3 gene (Pae2122) / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZVU2

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Non-polymers , 5 types, 1948 molecules

#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1888 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, glycerol, ammonium acetate, sodium acetate, cadmium chloride, sodium chloride, pH 8.0 VAPOR DIFFUSION, HANGING DROP at 293K
Crystal
*PLUS
Density Matthews: 2.6 Å3/Da
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
185 mg/mlprotein1drop
220 mMUMP1reservoir
310 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97954, 0.97933, 0.97186
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.979331
30.971861
ReflectionResolution: 2→100 Å / Num. all: 270937 / Num. obs: 270937 / % possible obs: 96.3 % / Observed criterion σ(F): -1.73 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.9 / Num. unique all: 21420 / % possible all: 76.3
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 1693038 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 76.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→19.97 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 13049 5 %RANDOM
Rwork0.191 ---
all0.191 262801 --
obs0.191 262801 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.434 Å2 / ksol: 0.377863 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.75 Å20 Å20 Å2
2---4.55 Å20 Å2
3----8.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28588 0 165 1888 30641
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.482.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 1711 4.9 %
Rwork0.283 32917 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOP
X-RAY DIFFRACTION5ACY.PARAMACY.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 4.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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