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- PDB-3sen: Structure of Caskin1 Tandem SAMs -

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Basic information

Entry
Database: PDB / ID: 3sen
TitleStructure of Caskin1 Tandem SAMs
ComponentsCaskin-1
KeywordsSIGNALING PROTEIN / SAM domain / Protein-Protein Interaction
Function / homology
Function and homology information


signal transduction / identical protein binding / cytoplasm
Similarity search - Function
Caskin-1, SH3 domain / Caskin, C-terminal / Caskin-1, CASK-interaction domain / Caskin1/2, SAM repeat 1 / Caskin1/2, SAM repeat 2 / Caskin1 CASK-interaction domain / C-terminal region of Caskin / Proline rich region of Caskin proteins / : / Transcription Factor, Ets-1 ...Caskin-1, SH3 domain / Caskin, C-terminal / Caskin-1, CASK-interaction domain / Caskin1/2, SAM repeat 1 / Caskin1/2, SAM repeat 2 / Caskin1 CASK-interaction domain / C-terminal region of Caskin / Proline rich region of Caskin proteins / : / Transcription Factor, Ets-1 / Variant SH3 domain / SAM domain (Sterile alpha motif) / Ankyrin repeats (many copies) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / DNA polymerase; domain 1 / Src homology 3 (SH3) domain profile. / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsStafford, R.L. / Bowie, J.U.
CitationJournal: Structure / Year: 2011
Title: Tandem SAM domain structure of human Caskin1: a presynaptic, self-assembling scaffold for CASK.
Authors: Stafford, R.L. / Hinde, E. / Knight, M.J. / Pennella, M.A. / Ear, J. / Digman, M.A. / Gratton, E. / Bowie, J.U.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 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 / 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

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Assembly

Deposited unit
A: Caskin-1
B: Caskin-1
C: Caskin-1
D: Caskin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6145
Polymers71,5744
Non-polymers391
Water0
1
A: Caskin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9332
Polymers17,8941
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Caskin-1


Theoretical massNumber of molelcules
Total (without water)17,8941
Polymers17,8941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Caskin-1


Theoretical massNumber of molelcules
Total (without water)17,8941
Polymers17,8941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Caskin-1


Theoretical massNumber of molelcules
Total (without water)17,8941
Polymers17,8941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.226, 94.597, 118.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A8 - 149
2114B8 - 149
1124C8 - 143
2124D8 - 143

NCS ensembles :
ID
1
2

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Components

#1: Protein
Caskin-1 / CASK-interacting protein 1


Mass: 17893.609 Da / Num. of mol.: 4 / Fragment: unp residues 470-613
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASKIN1, KIAA1306 / Plasmid: pQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q8WXD9
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

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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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM Na/K phosphate, 1-10% PEG 2K, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2010
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.1→100 Å / Num. obs: 19376 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.085 / Χ2: 1.056 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.2110.20.5918981.0761100
3.21-3.3410.20.39818941.0881100
3.34-3.4910.10.27319271.081100
3.49-3.6810.20.1718851.0661100
3.68-3.9110.10.12719221.0491100
3.91-4.21100.09619211.0781100
4.21-4.639.80.0819241.0261100
4.63-5.39.80.07319491.064199.9
5.3-6.689.80.06419781.0891100
6.68-1009.20.04320780.944199.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SEI

3sei


Resolution: 3.1→73.96 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.2951 / WRfactor Rwork: 0.2596 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8107 / SU B: 39.922 / SU ML: 0.34 / SU R Cruickshank DPI: 1.9229 / SU Rfree: 0.4371 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 980 5.1 %RANDOM
Rwork0.2399 ---
obs0.242 19233 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 351.68 Å2 / Biso mean: 136.113 Å2 / Biso min: 45.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å20 Å2
2--2.42 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 3.1→73.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 1 0 4392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224494
X-RAY DIFFRACTIONr_bond_other_d0.0040.023018
X-RAY DIFFRACTIONr_angle_refined_deg0.9071.9686105
X-RAY DIFFRACTIONr_angle_other_deg0.80737441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0845550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60825.193181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8615803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4061512
X-RAY DIFFRACTIONr_chiral_restr0.0490.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02826
X-RAY DIFFRACTIONr_mcbond_it4.6351.52762
X-RAY DIFFRACTIONr_mcbond_other0.3031.51108
X-RAY DIFFRACTIONr_mcangle_it8.22824460
X-RAY DIFFRACTIONr_scbond_it5.75431732
X-RAY DIFFRACTIONr_scangle_it10.2144.51645
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1860MEDIUM POSITIONAL0.330.5
1A1860MEDIUM THERMAL7.042
2C1818MEDIUM POSITIONAL0.420.5
2C1818MEDIUM THERMAL7.672
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 64 -
Rwork0.318 1259 -
all-1323 -
obs--93.5 %
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)
13.4699-1.94790.75430.4455-1.24760.6975-0.3797-0.20360.0009-0.02680.1924-0.02220.0454-0.06450.18730.51170.0222-0.15130.4495-0.00980.5012-23.67921.0860.456
21.01691.51682.64742.33012.06162.64060.2235-0.15620.2090.0828-0.58070.10880.336-0.07230.35710.4579-0.0079-0.08210.5327-0.28750.4667-45.4350.278-29.193
31.4881-2.62442.75161.2856-1.14482.58960.36510.5425-0.22170.1245-0.9293-0.19120.2178-0.01260.56420.43070.28720.13220.6943-0.13090.40782.1033.992-14.588
40.4392-2.5824-0.62972.6793-0.3956-0.473-0.06230.45940.45730.331-0.0821-0.05010.47280.67680.14430.251-0.0164-0.10880.76330.36750.5391-19.47141.639-17.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 149
2X-RAY DIFFRACTION1A150
3X-RAY DIFFRACTION2B8 - 146
4X-RAY DIFFRACTION3C8 - 143
5X-RAY DIFFRACTION4D8 - 144

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