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- PDB-4gli: Crystal Structure of Human SMN YG-Dimer -

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Basic information

Entry
Database: PDB / ID: 4gli
TitleCrystal Structure of Human SMN YG-Dimer
ComponentsMaltose-binding periplasmic protein, Survival motor neuron protein chimera
KeywordsSUGAR BINDING PROTEIN / SPLICING / Soluble Glycine Zipper
Function / homology
Function and homology information


Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity ...Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / Cajal body / spliceosomal snRNP assembly / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / DNA-templated transcription termination / cytoplasmic ribonucleoprotein granule / Z disc / snRNP Assembly / nervous system development / outer membrane-bounded periplasmic space / SARS-CoV-2 modulates host translation machinery / perikaryon / periplasmic space / nuclear body / neuron projection / axon / DNA damage response / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain ...SMN complex subunit Smn1 / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Survival motor neuron protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsMartin, R.S. / Perry, K. / Van Duyne, G.D.
CitationJournal: Structure / Year: 2012
Title: The survival motor neuron protein forms soluble glycine zipper oligomers.
Authors: Martin, R. / Gupta, K. / Ninan, N.S. / Perry, K. / Van Duyne, G.D.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, Survival motor neuron protein chimera


Theoretical massNumber of molelcules
Total (without water)44,4571
Polymers44,4571
Non-polymers00
Water2,882160
1
A: Maltose-binding periplasmic protein, Survival motor neuron protein chimera

A: Maltose-binding periplasmic protein, Survival motor neuron protein chimera


Theoretical massNumber of molelcules
Total (without water)88,9152
Polymers88,9152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2280 Å2
ΔGint-23 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.745, 65.914, 84.908
Angle α, β, γ (deg.)90.00, 110.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Maltose-binding periplasmic protein, Survival motor neuron protein chimera / MBP / MMBP / Maltodextrin-binding protein / Component of gems 1 / Gemin-1


Mass: 44457.305 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, SMN, SMN1, SMN2, SMNC, SMNT / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q16637
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS A CHIMERA COMPRISING MBP (UNP RESIDUES 27-395) AND THE C-TERMINAL DOMAIN (UNP RESIDUES ...PROTEIN IS A CHIMERA COMPRISING MBP (UNP RESIDUES 27-395) AND THE C-TERMINAL DOMAIN (UNP RESIDUES 263-294) OF SURVIVAL MOTOR NEURON PROTEIN.

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl, pH 8.0, 14% w/v PEG3350, 10 mM calcium chloride, 0.1 M potassium chloride, 0.1 M ammonium sulfate, 18% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.903→26.734 Å / Num. all: 35715 / Num. obs: 35714 / % possible obs: 99.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 25.075 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 19.7
Reflection shellHighest resolution: 1.903 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMP

1omp


Resolution: 1.903→26.734 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.664 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24709 -5 %RANDOM
Rwork0.20304 ---
all0.20533 35715 --
obs0.20533 35714 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.075 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å21.63 Å2
2---1.75 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 1.903→26.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 0 160 3193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223136
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.964258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5715393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30325.441136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86315530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.45157
X-RAY DIFFRACTIONr_chiral_restr0.1590.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212393
X-RAY DIFFRACTIONr_mcbond_it1.2571.51946
X-RAY DIFFRACTIONr_mcangle_it2.07323122
X-RAY DIFFRACTIONr_scbond_it3.38831190
X-RAY DIFFRACTIONr_scangle_it5.1054.51136
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 116 -
Rwork0.248 2175 -
obs--86.65 %

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