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- PDB-5mki: Crystal structure of SmAP (LSm) protein from Methanococcus vannielii -

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Basic information

Entry
Database: PDB / ID: 5mki
TitleCrystal structure of SmAP (LSm) protein from Methanococcus vannielii
ComponentsLike-Sm ribonucleoprotein core
KeywordsRNA BINDING PROTEIN / Lsm / SmAP
Function / homology
Function and homology information


ribonucleoprotein complex
Similarity search - Function
snRNP Sm-like, putative, archaea / 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
Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesMethanococcus vannielii SB (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.048 Å
AuthorsNikulin, A.D. / Lekontseva, N.V. / Tishchenko, S.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Scientific Foundation14-14-00496 Russian Federation
CitationJournal: Biochimie / Year: 2020
Title: Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode.
Authors: Lekontseva, N. / Mikhailina, A. / Fando, M. / Kravchenko, O. / Balobanov, V. / Tishchenko, S. / Nikulin, A.
History
DepositionDec 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Like-Sm ribonucleoprotein core
B: Like-Sm ribonucleoprotein core
C: Like-Sm ribonucleoprotein core
D: Like-Sm ribonucleoprotein core
E: Like-Sm ribonucleoprotein core
F: Like-Sm ribonucleoprotein core
G: Like-Sm ribonucleoprotein core
H: Like-Sm ribonucleoprotein core
I: Like-Sm ribonucleoprotein core
J: Like-Sm ribonucleoprotein core
K: Like-Sm ribonucleoprotein core
L: Like-Sm ribonucleoprotein core
M: Like-Sm ribonucleoprotein core
N: Like-Sm ribonucleoprotein core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,74525
Polymers114,10614
Non-polymers63911
Water8,863492
1
A: Like-Sm ribonucleoprotein core
B: Like-Sm ribonucleoprotein core
C: Like-Sm ribonucleoprotein core
D: Like-Sm ribonucleoprotein core
E: Like-Sm ribonucleoprotein core
F: Like-Sm ribonucleoprotein core
G: Like-Sm ribonucleoprotein core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,25412
Polymers57,0537
Non-polymers2005
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-125 kcal/mol
Surface area22510 Å2
MethodPISA
2
H: Like-Sm ribonucleoprotein core
I: Like-Sm ribonucleoprotein core
J: Like-Sm ribonucleoprotein core
K: Like-Sm ribonucleoprotein core
L: Like-Sm ribonucleoprotein core
M: Like-Sm ribonucleoprotein core
N: Like-Sm ribonucleoprotein core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,49213
Polymers57,0537
Non-polymers4396
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-103 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.671, 114.221, 71.993
Angle α, β, γ (deg.)90.00, 113.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Like-Sm ribonucleoprotein core


Mass: 8150.450 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus vannielii SB (archaea) / Gene: Mevan_0470 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A6UPF5
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: Protein 10 mg/ml, 30% PEG400, 0,1M HEPES, pH 7.5, 0,2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.048→50 Å / Num. all: 240673 / Num. obs: 63608 / % possible obs: 97.9 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.77
Reflection shellResolution: 2.048→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.638 / % possible all: 95.38

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I4K

1i4k


Resolution: 2.048→43.164 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.34
RfactorNum. reflection% reflection
Rfree0.2566 3163 4.98 %
Rwork0.1907 --
obs0.1939 63555 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.048→43.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7692 0 25 492 8209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077798
X-RAY DIFFRACTIONf_angle_d0.8810516
X-RAY DIFFRACTIONf_dihedral_angle_d5.5134993
X-RAY DIFFRACTIONf_chiral_restr0.0561241
X-RAY DIFFRACTIONf_plane_restr0.0041347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0476-2.07820.32281410.29372336X-RAY DIFFRACTION89
2.0782-2.11070.3341550.27872688X-RAY DIFFRACTION99
2.1107-2.14530.33731390.2662593X-RAY DIFFRACTION99
2.1453-2.18230.34671500.27212652X-RAY DIFFRACTION99
2.1823-2.22190.33971460.25482568X-RAY DIFFRACTION98
2.2219-2.26470.30141250.25672591X-RAY DIFFRACTION97
2.2647-2.31090.33451570.23752622X-RAY DIFFRACTION99
2.3109-2.36110.31471340.22132644X-RAY DIFFRACTION99
2.3611-2.41610.31331220.21632691X-RAY DIFFRACTION99
2.4161-2.47650.30011190.21362659X-RAY DIFFRACTION99
2.4765-2.54340.33811520.21752610X-RAY DIFFRACTION99
2.5434-2.61830.28071510.18952615X-RAY DIFFRACTION99
2.6183-2.70280.28711370.20072639X-RAY DIFFRACTION98
2.7028-2.79930.27671350.20092578X-RAY DIFFRACTION96
2.7993-2.91140.28881440.19852671X-RAY DIFFRACTION99
2.9114-3.04390.24541440.18612632X-RAY DIFFRACTION99
3.0439-3.20430.2741450.19932649X-RAY DIFFRACTION99
3.2043-3.4050.2121070.18032662X-RAY DIFFRACTION98
3.405-3.66780.23861130.16662649X-RAY DIFFRACTION97
3.6678-4.03660.22261240.16842657X-RAY DIFFRACTION99
4.0366-4.62020.20841390.13762674X-RAY DIFFRACTION99
4.6202-5.81870.20461100.15732663X-RAY DIFFRACTION98
5.8187-43.1740.20451740.18732649X-RAY DIFFRACTION98

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