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- PDB-4rg5: Crystal Structure of S. Pombe SMN YG-Dimer -

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Basic information

Entry
Database: PDB / ID: 4rg5
TitleCrystal Structure of S. Pombe SMN YG-Dimer
ComponentsMaltose-binding periplasmic protein, Survival Motor Neuron protein chimera
KeywordsSUGAR BINDING PROTEIN / SOLUBLE GLYCINE ZIPPER / SPLICING
Function / homology
Function and homology information


SMN complex / mRNA cis splicing, via spliceosome / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...SMN complex / mRNA cis splicing, via spliceosome / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / spliceosomal snRNP assembly / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / RNA binding / membrane / nucleus
Similarity search - Function
SMN complex subunit Smn1 / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / MALONATE ION / : / Maltose/maltodextrin-binding periplasmic protein / SMN complex subunit smn1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGupta, K. / Martin, R.S. / Sarachan, K.L. / Sharp, B. / Van Duyne, G.D.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Oligomeric Properties of Survival Motor NeuronGemin2 Complexes.
Authors: Gupta, K. / Martin, R. / Sharp, R. / Sarachan, K.L. / Ninan, N.S. / Van Duyne, G.D.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Maltose-binding periplasmic protein, Survival Motor Neuron protein chimera
B: Maltose-binding periplasmic protein, Survival Motor Neuron protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,38213
Polymers88,8202
Non-polymers1,56111
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-79 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.429, 105.015, 107.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailssecond part of the biological unit (a dimer) is Chain B / second part of the biological unit (a dimer) is Chain A

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Components

#1: Protein Maltose-binding periplasmic protein, Survival Motor Neuron protein chimera


Mass: 44410.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli)
References: UniProt: G4PNN1, UniProt: Q09808, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium malonate, pH5.6, 3.0M ammonium sulphate, 20% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 4, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 119228 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.89 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.01 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.301 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19223 5988 5 %RANDOM
Rwork0.16488 ---
obs0.16628 113240 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.931 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2---0.03 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 95 889 7245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.026512
X-RAY DIFFRACTIONr_angle_refined_deg2.2371.9788845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08925.603282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.205151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.941514
X-RAY DIFFRACTIONr_chiral_restr0.1840.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214904
X-RAY DIFFRACTIONr_mcbond_it2.2181.9053204
X-RAY DIFFRACTIONr_mcangle_it3.1312.844002
X-RAY DIFFRACTIONr_scbond_it4.4272.3513308
X-RAY DIFFRACTIONr_long_range_B_refined9.57718.70811234
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 392 -
Rwork0.273 7909 -
obs--94.35 %
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)
10.44880.1183-0.210.6662-0.17940.5689-0.0190.0129-0.0230.05470.02620.0353-0.04430.0112-0.00730.0256-0.0003-0.00380.0033-0.00590.0463-20.08110.3711.627
20.635-0.2102-0.03440.66530.25160.1499-0.0018-0.05570.01960.02790.0373-0.0177-0.0249-0.0193-0.03550.05210.0173-0.00210.03210.00850.05317.79-22.81-3.704
30.207-0.222-0.0220.47660.05420.0852-0.0219-0.0087-0.01440.0340.02530.0210.00840.0084-0.00340.0263-0.0095-0.0040.0148-0.00640.0503-6.736-5.7-2.039
420.2815-4.01941.81892.79882.17933.5957-0.3118-0.50340.11920.12580.2444-0.0044-0.06110.04670.06740.09870.03490.0030.09260.00090.102-18.5158.1721.673
51.657-5.885-1.720622.62836.93562.18210.0951-0.08710.1319-0.61480.0078-0.4165-0.2259-0.0483-0.10280.07150.0530.02770.09250.01340.05965.817-20.693-3.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 399
2X-RAY DIFFRACTION2B1 - 395
3X-RAY DIFFRACTION3A601 - 976
4X-RAY DIFFRACTION4A501
5X-RAY DIFFRACTION5B501

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