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- PDB-1loj: Crystal structure of a Methanobacterial Sm-like archaeal protein ... -

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Basic information

Entry
Database: PDB / ID: 1loj
TitleCrystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)
Componentssmall nuclear ribonucleoprotein homolog (Sm-like)
KeywordsRNA BINDING PROTEIN / transcription / beta barrel / OB-fold / heptameric toroid / tetradecamer
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
URIDINE-5'-MONOPHOSPHATE / URIDINE-5'-MONOPHOSPHATE / URIDINE / Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 6, 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: 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
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / struct_asym / struct_biol / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_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)
H: small nuclear ribonucleoprotein homolog (Sm-like)
I: small nuclear ribonucleoprotein homolog (Sm-like)
J: small nuclear ribonucleoprotein homolog (Sm-like)
K: small nuclear ribonucleoprotein homolog (Sm-like)
L: small nuclear ribonucleoprotein homolog (Sm-like)
M: small nuclear ribonucleoprotein homolog (Sm-like)
N: small nuclear ribonucleoprotein homolog (Sm-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,58442
Polymers135,03114
Non-polymers5,55328
Water6,972387
1
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)70,21221
Polymers67,5167
Non-polymers2,69714
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16080 Å2
ΔGint-123 kcal/mol
Surface area24380 Å2
MethodPISA
2
H: small nuclear ribonucleoprotein homolog (Sm-like)
I: small nuclear ribonucleoprotein homolog (Sm-like)
J: small nuclear ribonucleoprotein homolog (Sm-like)
K: small nuclear ribonucleoprotein homolog (Sm-like)
L: small nuclear ribonucleoprotein homolog (Sm-like)
M: small nuclear ribonucleoprotein homolog (Sm-like)
N: small nuclear ribonucleoprotein homolog (Sm-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,37221
Polymers67,5167
Non-polymers2,85714
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18770 Å2
ΔGint-149 kcal/mol
Surface area24020 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40670 Å2
ΔGint-271 kcal/mol
Surface area42580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.254, 109.956, 83.756
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe asymmetric unit contains a tetradecamer of SmAP1 monomers arranged with pseudo-72 point group symmetry. The biological assembly is thought to be the heptamer formed by chains A through G (or H through N). Any biological significance of the 14-mer in the asymmetric unit is unknown.

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Components

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Protein , 1 types, 14 molecules ABCDEFGHIJKLMN

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


Mass: 9645.075 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: full-length SmAP1 with additional 5-6 residues appended to the C-terminus (artefact of cloning vector)
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Species: Methanothermobacter thermautotrophicus / Strain: delta H / Gene: Mth649 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O26745

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Non-polymers , 5 types, 415 molecules

#2: Chemical
ChemComp-U / URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H12N2O6
#5: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, ammonium acetate, MPD, sodium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 293K

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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: Nov 20, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 89378 / Num. obs: 89378 / % possible obs: 97 % / Observed criterion σ(F): -1.73 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.8
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8488 / % possible all: 92.4

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Processing

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

1jbm


Resolution: 1.9→19.79 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: No NCS-restraints applied at any point in the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4364 5.1 %RANDOM
Rwork0.207 ---
all0.207 86242 --
obs0.207 86242 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.8996 Å2 / ksol: 0.339434 e/Å3
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å2-2.79 Å2
2--5.71 Å20 Å2
3----2.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8226 0 262 499 8987
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it2.021.5
X-RAY DIFFRACTIONc_mcangle_it3.222
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it4.152.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 639 5.1 %
Rwork0.299 11836 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MPD.PARAMMPD.TOP
X-RAY DIFFRACTION4CAM_URD.PARAMCAM_URD.TOP

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