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- PDB-1ljo: CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOB... -

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Basic information

Entry
Database: PDB / ID: 1ljo
TitleCRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION
ComponentsArchaeal Sm-like protein AF-Sm2
KeywordsUNKNOWN FUNCTION / SNRNP / SM / CORE SNRNP DOMAIN / RNA BINDING PROTEIN
Function / homology
Function and homology information


ribonucleoprotein complex / RNA binding
Similarity search - Function
SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / 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 / : / SnRNP, putative
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.95 Å
AuthorsToro, I. / Basquin, J. / Teo-Dreher, H. / Suck, D.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus.
Authors: Toro, I. / Basquin, J. / Teo-Dreher, H. / Suck, D.
#1: Journal: Embo J. / Year: 2001
Title: RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex.
Authors: Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Sraphin, B. / Suck, D.
History
DepositionApr 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 600HETEROGEN Cd ion sitting on six-fold axis is modelling a sulphate ion

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archaeal Sm-like protein AF-Sm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9105
Polymers8,6171
Non-polymers2934
Water59433
1
A: Archaeal Sm-like protein AF-Sm2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)53,45830
Polymers51,7026
Non-polymers1,75524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area11110 Å2
ΔGint-74 kcal/mol
Surface area20190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.420, 58.420, 32.084
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-78-

CD

21A-307-

HOH

31A-309-

HOH

41A-398-

HOH

51A-442-

HOH

61A-444-

HOH

DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: -Y,X-Y,Z; Y-X,-X,Z; -X,-Y,Z; Y,Y-X,Z and X-Y,X,Z

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Components

#1: Protein Archaeal Sm-like protein AF-Sm2


Mass: 8617.045 Da / Num. of mol.: 1 / Mutation: 'N-terminal GA added'
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0362 / Plasmid: modified pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29885
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.83 Å3/Da / Density % sol: 32.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: ammonium sulphate, lithium sulphate, sodium sulphate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
212 %(w/v)PEG60001reservoir
3100 mMsodium citrate1reservoirpH4.3

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF BM1411
ROTATING ANODEELLIOTT GX-2121.5418
Detector
TypeIDDetectorDate
MARRESEARCH1CCDApr 29, 1999
MARRESEARCH2IMAGE PLATEApr 20, 1999
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Ni MIRROR + Ni FILTERSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.54181
ReflectionResolution: 1.95→27.1 Å / Num. all: 4522 / Num. obs: 4522 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 18.567 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4.2 / Num. unique all: 598 / Rsym value: 0.173 / % possible all: 90.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 11984 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 90.9 % / Rmerge(I) obs: 0.173

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: Built by ARP/WARP (68 residues)

Resolution: 1.95→27.1 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD TARGET
RfactorNum. reflection% reflectionSelection details
Rfree0.211 226 5 %RANDOM
Rwork0.194 ---
all0.195 4681 --
obs0.195 4521 96.6 %-
Solvent computationSolvent model: flat model / Bsol: 56.1311 Å2 / ksol: 0.379594 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--5.74 Å2-1.46 Å20 Å2
2---5.74 Å20 Å2
3---11.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms578 0 13 33 624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005357
X-RAY DIFFRACTIONc_angle_deg1.32164
X-RAY DIFFRACTIONc_dihedral_angle_d25.47853
X-RAY DIFFRACTIONc_improper_angle_d0.72657
X-RAY DIFFRACTIONc_mcbond_it2.255
X-RAY DIFFRACTIONc_scbond_it3.077
X-RAY DIFFRACTIONc_mcangle_it3.363
X-RAY DIFFRACTIONc_scangle_it4.729
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 38 5.4 %
Rwork0.199 670 -
obs-708 91.5 %
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 DIFFRACTION4ACY.PARACY.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.195 / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.47853
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72657
LS refinement shell
*PLUS
Rfactor Rfree: 0.294 / Rfactor Rwork: 0.199

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