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- PDB-3bs7: Crystal structure of the Sterile Alpha Motif (SAM) domain of Hyph... -

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Basic information

Entry
Database: PDB / ID: 3bs7
TitleCrystal structure of the Sterile Alpha Motif (SAM) domain of Hyphen/Aveugle
ComponentsProtein aveugle
KeywordsSIGNALING PROTEIN / Sterile alpha motif (SAM) domain / Cytoplasm / Membrane / Sensory transduction / Vision
Function / homology
Function and homology information


Phosphorylation of CI / compound eye cone cell differentiation / Phosphorylation of SMO / compound eye photoreceptor cell differentiation / Phosphorylation of PER and TIM / eye photoreceptor cell differentiation / positive regulation of Ras protein signal transduction / cell surface receptor protein tyrosine kinase signaling pathway / visual perception / epidermal growth factor receptor signaling pathway ...Phosphorylation of CI / compound eye cone cell differentiation / Phosphorylation of SMO / compound eye photoreceptor cell differentiation / Phosphorylation of PER and TIM / eye photoreceptor cell differentiation / positive regulation of Ras protein signal transduction / cell surface receptor protein tyrosine kinase signaling pathway / visual perception / epidermal growth factor receptor signaling pathway / cytoplasmic side of plasma membrane / scaffold protein binding / positive regulation of ERK1 and ERK2 cascade / cytosol / cytoplasm
Similarity search - Function
Aveugle-like, SAM domain / : / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsRajakulendran, T. / Sicheri, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling.
Authors: Rajakulendran, T. / Sahmi, M. / Kurinov, I. / Tyers, M. / Therrien, M. / Sicheri, F.
History
DepositionDec 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Protein aveugle
B: Protein aveugle


Theoretical massNumber of molelcules
Total (without water)18,9762
Polymers18,9762
Non-polymers00
Water5,224290
1
A: Protein aveugle


Theoretical massNumber of molelcules
Total (without water)9,4881
Polymers9,4881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein aveugle


Theoretical massNumber of molelcules
Total (without water)9,4881
Polymers9,4881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.005, 88.470, 73.279
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

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Components

#1: Protein Protein aveugle


Mass: 9487.867 Da / Num. of mol.: 2
Fragment: Sterile Alpha Motif (SAM) domain; UNP residues 21-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ave / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ML92
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M Sodium citrate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2006
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.9→19.88 Å / Num. obs: 14692 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.9→1.95 Å / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.88 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.851 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 735 5 %RANDOM
Rwork0.214 ---
all0.217 14633 --
obs0.217 14633 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.095 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 0 290 1566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211309
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9261764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8395149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27722.11371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9615248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.041518
X-RAY DIFFRACTIONr_chiral_restr0.1010.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02980
X-RAY DIFFRACTIONr_nbd_refined0.3260.2772
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3150.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4120.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.233
X-RAY DIFFRACTIONr_mcbond_it1.2721.5774
X-RAY DIFFRACTIONr_mcangle_it1.94221208
X-RAY DIFFRACTIONr_scbond_it3.3993637
X-RAY DIFFRACTIONr_scangle_it5.0434.5556
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 52 -
Rwork0.221 1015 -
all-1067 -
obs--100 %

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