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- PDB-4nl9: Crystal structure of the human Anks3-SAM/Anks6-SAM heterodimer -

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Basic information

Entry
Database: PDB / ID: 4nl9
TitleCrystal structure of the human Anks3-SAM/Anks6-SAM heterodimer
Components
  • Ankyrin repeat and SAM domain-containing protein 3
  • Ankyrin repeat and SAM domain-containing protein 6
KeywordsSTRUCTURAL PROTEIN / SAM domain / protein-protein interaction domain / heterodimer / SamCystin / polycystic kidney disease
Function / homology
Function and homology information


embryo development ending in birth or egg hatching / cilium / cytoplasm
Similarity search - Function
: / : / Domain of unknown function DUF3447 / Transcription Factor, Ets-1 / 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 ...: / : / Domain of unknown function DUF3447 / Transcription Factor, Ets-1 / 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 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ankyrin repeat and SAM domain-containing protein 6 / Ankyrin repeat and SAM domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLeettola, C.N. / Cascio, D. / Bowie, J.U.
CitationJournal: Bmc Struct.Biol. / Year: 2014
Title: Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3.
Authors: Leettola, C.N. / Knight, M.J. / Cascio, D. / Hoffman, S. / Bowie, J.U.
History
DepositionNov 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin repeat and SAM domain-containing protein 3
B: Ankyrin repeat and SAM domain-containing protein 3
C: Ankyrin repeat and SAM domain-containing protein 6
D: Ankyrin repeat and SAM domain-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9105
Polymers31,8864
Non-polymers241
Water4,432246
1
A: Ankyrin repeat and SAM domain-containing protein 3
C: Ankyrin repeat and SAM domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)15,9432
Polymers15,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ankyrin repeat and SAM domain-containing protein 3
D: Ankyrin repeat and SAM domain-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9673
Polymers15,9432
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.700, 108.520, 101.740
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
11C-122-

HOH

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Components

#1: Protein Ankyrin repeat and SAM domain-containing protein 3


Mass: 8050.185 Da / Num. of mol.: 2 / Fragment: SAM Domain, UNP residues 421- 490 / Mutation: I36E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANKS3, KIAA1977 / Plasmid: pHis-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q6ZW76
#2: Protein Ankyrin repeat and SAM domain-containing protein 6 / Ankyrin repeat domain-containing protein 14 / SamCystin / Sterile alpha motif domain-containing ...Ankyrin repeat domain-containing protein 14 / SamCystin / Sterile alpha motif domain-containing protein 6 / SAM domain-containing protein 6


Mass: 7892.806 Da / Num. of mol.: 2 / Fragment: SAM Domain, UNP residues 771-840
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRD14, ANKS6, PKDR1, SAMD6 / Plasmid: pHis-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q68DC2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop, streak seeding / pH: 8
Details: 31.5% PEG-4000, 100mM Tris, 0.25M magnesium chloride, pH 8.0, vapor diffusion, hanging drop, streak seeding, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 42244 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.32 % / Biso Wilson estimate: 16.68 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.540.3714.16150353042196.9
1.54-1.580.3235.17167293030199.8
1.58-1.630.2815.99164402956199.9
1.63-1.680.2297156082868199.7
1.68-1.730.1967.87143122794199.7
1.73-1.790.1729.53152142709199.8
1.79-1.860.1411.34146662618199.9
1.86-1.940.13212.57128112442197.3
1.94-2.020.09915.2126522391199.1
2.02-2.120.08317.25118602315199.4
2.12-2.230.07420.06119882177199.5
2.23-2.370.06921.3106602063197
2.37-2.530.06222.51102051931199.3
2.53-2.740.05723.5490741818198.2
2.74-30.05426.0292841701199.4
3-3.350.04928.181041511198.8
3.35-3.870.04828.3365941337196.5
3.87-4.740.04430.9562501138196.6
4.74-6.70.04229.884835895195.8
6.7-1000.03930.482651508191.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.88 Å
Translation2.5 Å47.88 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4NJ8

4nj8


Resolution: 1.5→50.87 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8701 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 4221 10 %RANDOM
Rwork0.1798 ---
obs0.1823 42203 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.23 Å2 / Biso mean: 22.7039 Å2 / Biso min: 11.85 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 1 246 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051975
X-RAY DIFFRACTIONf_angle_d0.9442657
X-RAY DIFFRACTIONf_chiral_restr0.06310
X-RAY DIFFRACTIONf_plane_restr0.004340
X-RAY DIFFRACTIONf_dihedral_angle_d13.472753
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.5-1.5160.21921320.21211881320132093
1.516-1.53390.2381390.1969124713861386100
1.5339-1.55260.25531420.193127714191419100
1.5526-1.57220.22361390.1816124813871387100
1.5722-1.59290.21461420.1916128414261426100
1.5929-1.61480.21461400.18125513951395100
1.6148-1.63780.22721420.1805128214241424100
1.6378-1.66230.21531390.1843125113901390100
1.6623-1.68830.23041400.1828126214021402100
1.6883-1.71590.22911410.182126414051405100
1.7159-1.74550.22421410.187612671408140899
1.7455-1.77730.2281400.1917126414041404100
1.7773-1.81140.23231430.1839129014331433100
1.8114-1.84840.22711410.1953126414051405100
1.8484-1.88860.22381400.1931125613961396100
1.8886-1.93260.29311370.221412411378137896
1.9326-1.98090.25131400.191812531393139399
1.9809-2.03440.19011410.18412711412141299
2.0344-2.09430.18731410.182712661407140799
2.0943-2.16190.1961410.165812731414141499
2.1619-2.23920.18041400.17126314031403100
2.2392-2.32880.23661370.189112361373137396
2.3288-2.43480.20651410.178812711412141299
2.4348-2.56320.22941430.18412881431143199
2.5632-2.72380.22411410.192712681409140998
2.7238-2.93410.23831440.200712901434143499
2.9341-3.22930.23811430.19112881431143199
3.2293-3.69640.16811420.169212811423142397
3.6964-4.65660.15621420.143912751417141796
4.6566-50.89930.16421470.171413191466146694
Refinement TLS params.Method: refined / Origin x: -6.014 Å / Origin y: -24.3786 Å / Origin z: 13.6514 Å
111213212223313233
T0.1585 Å2-0.02 Å2-0.0092 Å2-0.1573 Å2-0.005 Å2--0.1216 Å2
L0.9207 °2-0.1751 °2-0.0621 °2-0.5266 °20.1174 °2--0.4278 °2
S0.0084 Å °0.0263 Å °-0.0233 Å °-0.014 Å °-0.0153 Å °-0.0047 Å °-0.0102 Å °0.0368 Å °0.0074 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 66
2X-RAY DIFFRACTION1allB7 - 69
3X-RAY DIFFRACTION1allC8 - 67
4X-RAY DIFFRACTION1allD7 - 67
5X-RAY DIFFRACTION1allB - C1 - 246
6X-RAY DIFFRACTION1allD1 - 101

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