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- PDB-3k3v: Crystal structure the GYF domain of S. Cerevisiae SMY2 -

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Basic information

Entry
Database: PDB / ID: 3k3v
TitleCrystal structure the GYF domain of S. Cerevisiae SMY2
ComponentsProtein SMY2
KeywordsPROTEIN BINDING / GYF domain / poly-proline binding / domain swap / RAGNYA / SMY2 / Phosphoprotein
Function / homology
Function and homology information


endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum membrane / cytosol / cytoplasm
Similarity search - Function
GYF domain / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAsh, M.R. / Faelber, K.
CitationJournal: To be Published
Title: SMY2-type GYF domain recognition in mRNA surveillance complexes
Authors: Ash, M.R. / Faelber, K. / Kosslick, D. / Albert, G. / Roske, Y. / Freund, C.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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: Protein SMY2


Theoretical massNumber of molelcules
Total (without water)11,1091
Polymers11,1091
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein SMY2

A: Protein SMY2


Theoretical massNumber of molelcules
Total (without water)22,2192
Polymers22,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area2570 Å2
ΔGint-27 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.400, 68.400, 111.321
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Protein SMY2 / Suppressor of MYO2-66 protein


Mass: 11109.328 Da / Num. of mol.: 1 / Fragment: GYF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMY2 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32909
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% polyacrylic acid, 0.15M MgCl2, 0.1M Na-HEPES, pH 7.5, Vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→25.19 Å / Num. all: 14884 / Num. obs: 14884 / % possible obs: 99.8 % / Redundancy: 20.9 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 31.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 5.2 / Num. measured all: 42500 / Num. unique all: 2107 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.5.0063refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FMA

3fma


Resolution: 1.8→25.19 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 4.467 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 747 5 %RANDOM
Rwork0.208 ---
all-14837 --
obs-14837 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 38.93 Å2 / Biso mean: 15.654 Å2 / Biso min: 6.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å20 Å2
2---0.29 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 0 0 84 723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022682
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.944932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.427586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98424.51631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32415117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.912152
X-RAY DIFFRACTIONr_chiral_restr0.0880.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021517
X-RAY DIFFRACTIONr_mcbond_it1.512405
X-RAY DIFFRACTIONr_mcangle_it2.3043665
X-RAY DIFFRACTIONr_scbond_it2.3663277
X-RAY DIFFRACTIONr_scangle_it3.4153.5264
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 57 -
Rwork0.235 998 -
all-1055 -
obs-1055 99.62 %
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)
10.4283-0.02820.09792.1693-0.29231.84280.04140.0359-0.0125-0.0994-0.03470.1155-0.04090.0651-0.00660.1120.0237-0.01460.09930.0050.1165-19.2648.516-7.434
23.5263-1.28310.58226.918-0.78823.4035-0.08650.0266-0.2260.13980.1271-0.25660.20130.4444-0.04060.11140.0806-0.00310.15050.02060.1091-27.41130.503-7.68
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 77
2X-RAY DIFFRACTION2A78 - 93

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