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- PDB-1mgq: CRYSTAL STRUCTURE OF A HEPTAMERIC SM-LIKE PROTEIN FROM METHANOBAC... -

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Basic information

Entry
Database: PDB / ID: 1mgq
TitleCRYSTAL STRUCTURE OF A HEPTAMERIC SM-LIKE PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
ComponentsSM-LIKE PROTEIN
KeywordsRNA BINDING PROTEIN / LSM / RNA-BINDING / ARCHEA
Function / homology
Function and homology information


Sm-like protein family complex / intracellular organelle / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCollins, B.M. / Naidoo, N. / Harrop, S.J. / Curmi, P.M.G. / Mabbutt, B.C.
Citation
Journal: To be published
Title: Refined Structure of Sm-Like Protein Heptamer from Methanobacterium thermoautotrophicum
Authors: Collins, B.M. / Naidoo, N. / Harrop, S.J. / Curmi, P.M.G. / Mabbutt, B.C.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of a Heptameric Sm-like Protein Complex from Archaea: Implications for the Structure and Evolution of snRNPs
Authors: Collins, B.M. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M.G. / Mabbutt, B.C.
History
DepositionAug 16, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SM-LIKE PROTEIN
B: SM-LIKE PROTEIN
C: SM-LIKE PROTEIN
D: SM-LIKE PROTEIN
E: SM-LIKE PROTEIN
F: SM-LIKE PROTEIN
G: SM-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)64,2917
Polymers64,2917
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-41 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.591, 71.883, 95.095
Angle α, β, γ (deg.)90.00, 94.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SM-LIKE PROTEIN / snRNP Sm-like protein


Mass: 9184.438 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: MT0649 / Plasmid: PGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O26745
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.31 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350, TRIS, LITHIUM SULPHATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 20, 2000
RadiationMonochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.7→40.49 Å / Num. obs: 59871 / Observed criterion σ(I): 3
Reflection shellResolution: 1.7→1.79 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I81

1i81


Resolution: 1.7→14.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.379 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.131 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 3021 5.1 %RANDOM
Rwork0.2292 ---
all0.2309 59928 --
obs0.2309 56448 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.512 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→14.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4022 0 0 251 4273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9925485
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8853504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4115798
X-RAY DIFFRACTIONr_chiral_restr0.1350.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023049
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.31882
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5454
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.344
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5170.521
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0441.52534
X-RAY DIFFRACTIONr_mcangle_it1.72924100
X-RAY DIFFRACTIONr_scbond_it2.65131530
X-RAY DIFFRACTIONr_scangle_it4.2854.51385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 195
Rwork0.284 4014
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4075-0.8052.64783.3983-1.78895.91690.1404-0.1181-0.15650.2565-0.0976-0.14750.46880.2937-0.04280.1228-0.00230.00670.14340.00510.164513.2703-19.327414.6974
22.1756-0.9133-0.59895.29270.82131.5742-0.03790.04670.13050.05860.0242-0.2802-0.0940.17510.01360.009-0.028-0.00270.08790.00470.117712.7327-5.16872.8212
32.9128-0.73540.13743.9594-0.73184.0956-0.1121-0.1470.17020.33860.0591-0.2539-0.17710.05950.05310.0172-0.0083-0.01890.0512-0.00080.140510.590912.60396.5564
43.72020.2199-0.60394.4402-2.06798.85720.0319-0.42950.30770.56240.0383-0.1157-0.75280.1915-0.07020.3260.0503-0.01420.1874-0.06660.16478.221720.755922.5798
53.0022-0.9979-0.49468.1250.73226.06020.0552-0.23720.10680.7337-0.07720.0807-0.24220.03760.02210.48150.05330.02170.2862-0.03450.08977.636813.384139.3104
63.4358-1.724-0.114611.9682.89267.1542-0.2949-0.2519-0.04721.67390.1846-0.05680.23480.01560.11030.73150.07360.04110.26680.00960.107310.2145-3.415944.247
73.0551-0.70720.09387.43961.735111.5102-0.1158-0.1246-0.10291.08460.0689-0.04210.64940.05430.04690.4472-0.01270.04430.20280.02990.108112.5749-18.556933.2219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 8110 - 83
2X-RAY DIFFRACTION2BB8 - 8110 - 83
3X-RAY DIFFRACTION3CC8 - 8110 - 83
4X-RAY DIFFRACTION4DD9 - 8111 - 83
5X-RAY DIFFRACTION5EE9 - 8111 - 83
6X-RAY DIFFRACTION6FF12 - 8114 - 83
7X-RAY DIFFRACTION7GG9 - 8111 - 83

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