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- PDB-1h64: CRYSTAL STRUCTURE OF THE SM-RELATED PROTEIN OF P. ABYSSI: THE BIO... -

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Basic information

Entry
Database: PDB / ID: 1h64
TitleCRYSTAL STRUCTURE OF THE SM-RELATED PROTEIN OF P. ABYSSI: THE BIOLOGICAL UNIT IS A HEPTAMER
ComponentsSNRNP SM-LIKE PROTEIN
KeywordsSM-LIKE PROTEIN / SM FOLD / SPLICEOSOME / SNRNP CORE
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
Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMayer, C. / Weeks, S. / Suck, D.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structures of the Pyrococcus Abyssi Sm Core and its Complex with RNA.Common Features of RNA Binding in Archaea and Eukarya
Authors: Thore, S. / Mayer, C. / Sauter, C. / Weeks, S. / Suck, D.
History
DepositionJun 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS AA, BB, CC AND DD ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS AA, BB, CC AND DD ON SHEET RECORDS BELOW IS ACTUALLY AN 35-STRANDED BARREL THIS IS REPRESENTED BY A 36-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. EACH SHEET INCORPORATES STRANDS FROM 7 CHAINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: SNRNP SM-LIKE PROTEIN
2: SNRNP SM-LIKE PROTEIN
A: SNRNP SM-LIKE PROTEIN
B: SNRNP SM-LIKE PROTEIN
C: SNRNP SM-LIKE PROTEIN
D: SNRNP SM-LIKE PROTEIN
E: SNRNP SM-LIKE PROTEIN
F: SNRNP SM-LIKE PROTEIN
G: SNRNP SM-LIKE PROTEIN
H: SNRNP SM-LIKE PROTEIN
I: SNRNP SM-LIKE PROTEIN
J: SNRNP SM-LIKE PROTEIN
K: SNRNP SM-LIKE PROTEIN
L: SNRNP SM-LIKE PROTEIN
M: SNRNP SM-LIKE PROTEIN
N: SNRNP SM-LIKE PROTEIN
O: SNRNP SM-LIKE PROTEIN
P: SNRNP SM-LIKE PROTEIN
Q: SNRNP SM-LIKE PROTEIN
R: SNRNP SM-LIKE PROTEIN
S: SNRNP SM-LIKE PROTEIN
T: SNRNP SM-LIKE PROTEIN
U: SNRNP SM-LIKE PROTEIN
V: SNRNP SM-LIKE PROTEIN
W: SNRNP SM-LIKE PROTEIN
X: SNRNP SM-LIKE PROTEIN
Y: SNRNP SM-LIKE PROTEIN
Z: SNRNP SM-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)238,05328
Polymers238,05328
Non-polymers00
Water24,1581341
1
A: SNRNP SM-LIKE PROTEIN
B: SNRNP SM-LIKE PROTEIN
C: SNRNP SM-LIKE PROTEIN
D: SNRNP SM-LIKE PROTEIN
E: SNRNP SM-LIKE PROTEIN
F: SNRNP SM-LIKE PROTEIN
G: SNRNP SM-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,5137
Polymers59,5137
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
H: SNRNP SM-LIKE PROTEIN
I: SNRNP SM-LIKE PROTEIN
J: SNRNP SM-LIKE PROTEIN
K: SNRNP SM-LIKE PROTEIN
L: SNRNP SM-LIKE PROTEIN
M: SNRNP SM-LIKE PROTEIN
N: SNRNP SM-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,5137
Polymers59,5137
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
O: SNRNP SM-LIKE PROTEIN
P: SNRNP SM-LIKE PROTEIN
Q: SNRNP SM-LIKE PROTEIN
R: SNRNP SM-LIKE PROTEIN
S: SNRNP SM-LIKE PROTEIN
T: SNRNP SM-LIKE PROTEIN
U: SNRNP SM-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,5137
Polymers59,5137
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
1: SNRNP SM-LIKE PROTEIN
2: SNRNP SM-LIKE PROTEIN
V: SNRNP SM-LIKE PROTEIN
W: SNRNP SM-LIKE PROTEIN
X: SNRNP SM-LIKE PROTEIN
Y: SNRNP SM-LIKE PROTEIN
Z: SNRNP SM-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,5137
Polymers59,5137
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.330, 70.160, 116.010
Angle α, β, γ (deg.)90.21, 97.70, 107.48
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.96925, 0.01261, -0.24575), (0.17899, 0.64921, 0.73925), (0.16886, -0.76051, 0.62699)-0.37596, 0.08035, -0.33448
2given(0.89638, 0.20894, -0.39095), (0.42233, -0.13462, 0.89639), (0.13466, -0.96862, -0.20892)-0.56783, -0.12662, -0.69871
3given(0.81879, 0.47823, -0.31762), (0.56972, -0.74503, 0.34692), (-0.07073, -0.46501, -0.88248)-0.05814, -0.49562, -0.75696
4given(0.80922, 0.58455, -0.0588), (0.48869, -0.72528, -0.48492), (-0.32611, 0.36368, -0.87258)0.24709, -0.60208, -0.42474
5given(0.8861, 0.43019, 0.17251), (0.2365, -0.09956, -0.96652), (-0.39861, 0.89723, -0.18996)0.05949, -0.39274, -0.2481
6given(0.9649, 0.18106, 0.19024), (0.02259, 0.66446, -0.74698), (-0.26165, 0.72506, 0.63705)0.0832, -0.32161, -0.09558
7given(-0.86978, -0.47175, -0.14468), (-0.47349, 0.71541, 0.5138), (-0.13888, 0.5154, -0.84562)32.21937, 9.6713, -3.85095
8given(-0.95542, -0.21836, -0.19872), (-0.21803, 0.06798, 0.97357), (-0.19908, 0.9735, -0.11256)32.31208, 9.55253, -3.79621
9given(-0.99952, -0.01229, -0.02842), (-0.01182, -0.69682, 0.71715), (-0.02862, 0.71714, 0.69634)32.39779, 9.41643, -3.92335
10given(-0.97382, -0.01075, 0.22707), (0.0005, -0.99898, -0.04517), (0.22733, -0.04387, 0.97283)32.64457, 9.28878, -3.79961
11given(-0.90316, -0.18226, 0.3887), (-0.19716, -0.62819, -0.75267), (0.38136, -0.75641, 0.53142)33.00585, 9.1211, -3.99005
12given(-0.82769, -0.45709, 0.32558), (-0.43457, 0.15496, -0.88721), (0.35508, -0.87582, -0.3269)32.60447, 9.28136, -4.38224
13given(-0.81137, -0.57338, 0.11364), (-0.57787, 0.75755, -0.30362), (0.088, -0.31202, -0.94599)32.16336, 9.5934, -3.8579
14given(1, 0.00165, 0.00175), (-0.00181, 0.99558, 0.09388), (-0.00159, -0.09388, 0.99558)-18.36445, 30.76265, 57.44737
15given(0.96771, 0.00214, -0.25207), (0.20419, 0.57971, 0.78882), (0.14782, -0.81482, 0.56055)-18.9376, 30.69783, 57.37962
16given(0.89117, 0.21695, -0.39844), (0.44226, -0.21969, 0.86956), (0.10112, -0.95114, -0.29173)-18.85553, 30.50577, 57.13132
17given(0.81366, 0.48484, -0.32075), (0.56802, -0.78049, 0.26115), (-0.12373, -0.39468, -0.91045)-18.34481, 30.33066, 57.18863
18given(0.80712, 0.58742, -0.05912), (0.46147, -0.69016, -0.55743), (-0.36824, 0.42263, -0.82812)-18.14046, 30.27676, 57.33345
19given(0.88462, 0.43186, 0.17592), (0.20531, -0.02197, -0.97845), (-0.41869, 0.90167, -0.1081)-18.35195, 30.49455, 57.39023
20given(0.96529, 0.18927, 0.18), (-0.01283, 0.72266, -0.69108), (-0.26088, 0.66478, 0.7)-18.14865, 30.72323, 57.45023
21given(-0.8677, -0.4744, -0.14847), (-0.48854, 0.75869, 0.43096), (-0.0918, 0.44648, -0.89007)13.77357, 40.27015, 53.05895
22given(-0.95407, -0.21916, -0.20424), (-0.24357, 0.17055, 0.95477), (-0.17442, 0.96067, -0.2161)13.95538, 40.40304, 53.33085
23given(-0.99916, -0.02658, -0.03105), (-0.00784, -0.62094, 0.78382), (-0.04012, 0.78341, 0.62021)13.82181, 39.87647, 53.50316
24given(-0.9772, -0.00085, 0.21233), (0.00718, -0.99955, 0.02902), (0.21221, 0.02988, 0.97677)14.44118, 39.84622, 53.32084
25given(-0.90915, -0.16566, 0.38211), (-0.17158, -0.68703, -0.70608), (0.3795, -0.70749, 0.59619)14.97204, 39.42363, 53.2173
26given(-0.82628, -0.46017, 0.32482), (-0.40895, 0.09355, -0.90775), (0.38733, -0.88289, -0.26548)14.16877, 39.7438, 52.69448
27given(-0.80735, -0.57988, 0.1092), (-0.57333, 0.72713, -0.37759), (0.13956, -0.36745, -0.91951)13.63387, 39.97965, 53.15086

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Components

#1: Protein ...
SNRNP SM-LIKE PROTEIN


Mass: 8501.899 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Description: GENOMIC DNA / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9V0Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1341 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 6.5 / Details: MPD, MAGNESIUM ACETATE, pH 6.50
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
127-29 %MPD1reservoir
2150 mMmagnesium acetate1reservoir
350 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→44 Å / Num. obs: 156432 / % possible obs: 96.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 14
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 156396 / % possible obs: 96.2 % / Num. measured all: 386356
Reflection shell
*PLUS
% possible obs: 95.2 % / Mean I/σ(I) obs: 7.5

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODELLED HEPTAMER

Resolution: 1.9→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.281 7850 5 %RANDOM
Rwork0.237 ---
obs0.237 156396 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0.85 Å20.64 Å2
2---0.77 Å2-0.44 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15820 0 0 1341 17161
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.71.5
X-RAY DIFFRACTIONc_mcangle_it3.772
X-RAY DIFFRACTIONc_scbond_it3.692
X-RAY DIFFRACTIONc_scangle_it5.432.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.305 781 0.053 %
Rwork0.274 14686 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Rfactor Rfree: 0.282
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS

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