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- PDB-1lnx: Crystal structure of the P.aerophilum SmAP1 heptamer in a new cry... -

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Basic information

Entry
Database: PDB / ID: 1lnx
TitleCrystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)
Componentssmall nuclear ribonucleoprotein homolog (Sm-like)
KeywordsRNA BINDING PROTEIN / transcription / beta barrel-like structure (OB fold) / homoheptameric
Function / homology
Function and homology information


mRNA processing / ribonucleoprotein complex / RNA binding
Similarity search - Function
snRNP Sm-like, putative, archaea / U6 snRNA-associated Sm-like protein Lsm1/8 / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...snRNP Sm-like, putative, archaea / U6 snRNA-associated Sm-like protein Lsm1/8 / SH3 type barrels. - #100 / 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 / URIDINE / Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMura, C. / Kozhukhovsky, A. / Eisenberg, D.
Citation
Journal: 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.
#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
DepositionMay 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 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: small nuclear ribonucleoprotein homolog (Sm-like)
B: small nuclear ribonucleoprotein homolog (Sm-like)
C: small nuclear ribonucleoprotein homolog (Sm-like)
D: small nuclear ribonucleoprotein homolog (Sm-like)
E: small nuclear ribonucleoprotein homolog (Sm-like)
F: small nuclear ribonucleoprotein homolog (Sm-like)
G: small nuclear ribonucleoprotein homolog (Sm-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,31126
Polymers62,5617
Non-polymers2,75019
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17010 Å2
ΔGint-48 kcal/mol
Surface area23500 Å2
MethodPISA
2
A: small nuclear ribonucleoprotein homolog (Sm-like)
B: small nuclear ribonucleoprotein homolog (Sm-like)
C: small nuclear ribonucleoprotein homolog (Sm-like)
D: small nuclear ribonucleoprotein homolog (Sm-like)
E: small nuclear ribonucleoprotein homolog (Sm-like)
F: small nuclear ribonucleoprotein homolog (Sm-like)
G: small nuclear ribonucleoprotein homolog (Sm-like)
hetero molecules

A: small nuclear ribonucleoprotein homolog (Sm-like)
B: small nuclear ribonucleoprotein homolog (Sm-like)
C: small nuclear ribonucleoprotein homolog (Sm-like)
D: small nuclear ribonucleoprotein homolog (Sm-like)
E: small nuclear ribonucleoprotein homolog (Sm-like)
F: small nuclear ribonucleoprotein homolog (Sm-like)
G: small nuclear ribonucleoprotein homolog (Sm-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,62352
Polymers125,12214
Non-polymers5,50138
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area47330 Å2
ΔGint-136 kcal/mol
Surface area33690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.829, 113.764, 126.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-8101-

ACY

21D-8266-

HOH

DetailsThe asymmetric unit contains the likely biologically relevant oligomer (heptamer). A 14-mer may be important, and is created by one of the crystallographic 2-folds (x, -y, -z).

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Components

#1: Protein
small nuclear ribonucleoprotein homolog (Sm-like) / Sm-like archaeal protein SmAP1


Mass: 8937.272 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: SmAP1, GPA2549 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZYG5
#2: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.61 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: sodium acetate, ammonium acetate, PEG 4000, glycerol, uridine-5'-monophosphate, dithiothreitol, pH 8.2, VAPOR DIFFUSION, HANGING DROP at 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2001 / Details: Osmic 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: 2.05→100 Å / Num. all: 40722 / Num. obs: 40722 / % possible obs: 97.4 % / Observed criterion σ(F): -1.73 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 17.9
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3949 / % possible all: 95.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I8F

1i8f


Resolution: 2.05→19.78 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2005 5 %RANDOM
Rwork0.182 ---
all0.182 39951 --
obs0.182 39951 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3041 Å2 / ksol: 0.357027 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å20 Å2
2--5.68 Å20 Å2
3----7.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 187 325 4519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.662
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 341 5.5 %
Rwork0.209 5902 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACY.PARAMACY.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOP
X-RAY DIFFRACTION5URD.PARAMURD.TOP

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