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- PDB-4nj8: Crystal structure of the human ANKS3 SAM Domain L52A mutant -

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Basic information

Entry
Database: PDB / ID: 4nj8
TitleCrystal structure of the human ANKS3 SAM Domain L52A mutant
ComponentsAnkyrin repeat and SAM domain-containing protein 3
KeywordsSTRUCTURAL PROTEIN / SAM domain / protein-protein interaction domain / polymerization domain
Function / homology
Function and homology information


: / : / 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) ...: / : / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Ankyrin repeat and SAM domain-containing protein 3
B: Ankyrin repeat and SAM domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)15,9842
Polymers15,9842
Non-polymers00
Water90150
1
A: Ankyrin repeat and SAM domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)7,9921
Polymers7,9921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ankyrin repeat and SAM domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)7,9921
Polymers7,9921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.890, 71.890, 33.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 7992.149 Da / Num. of mol.: 2 / Fragment: SAM Domain, UNP residues 421- 490 / Mutation: L52A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 15% PEG-8000, 100mM sodium/potassium phosphate, 0.3M sodium chloride, pH 6.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 22798 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 15.15 % / Biso Wilson estimate: 35.344 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.11
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.640.7775.4246311640199.3
1.64-1.690.5967.1248101607197.9
1.69-1.730.448.862437815891100
1.73-1.790.33910.35235171562198.5
1.79-1.850.2413.04221791508199.8
1.85-1.910.19715.7226721410199
1.91-1.980.15618.55218961411199.2
1.98-2.060.11821.072073713421100
2.06-2.160.10323.04190651294199.4
2.16-2.260.09425.71184581229198.4
2.26-2.380.08527.821895811941100
2.38-2.530.08428.66172791112199.8
2.53-2.70.07729.79158971057199.9
2.7-2.920.07630.2214105979198.7
2.92-3.20.07432.28140369081100
3.2-3.580.07632.24125108411100
3.58-4.130.07331.349952718198.4
4.13-5.060.07332.989465624199.8
5.06-7.150.07632.367257495199.8
7.15-1000.10630.593669278196.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.32 Å71.89 Å
Translation5.32 Å71.89 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→71.89 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 2280 10 %RANDOM
Rwork0.1975 ---
obs0.1995 22797 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.89 Å2 / Biso mean: 37.4836 Å2 / Biso min: 17.85 Å2
Refinement stepCycle: LAST / Resolution: 1.6→71.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 0 50 1072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_plane_restr0.004
X-RAY DIFFRACTIONf_chiral_restr0.035
X-RAY DIFFRACTIONf_dihedral_angle_d11.932
X-RAY DIFFRACTIONf_angle_d0.92
X-RAY DIFFRACTIONf_bond_d0.006
LS refinement shellResolution: 1.6→1.634 Å
RfactorNum. reflection% reflection
Rfree0.257 138 -
Rwork0.2582 --
obs-1379 99 %
Refinement TLS params.Method: refined / Origin x: -11.4956 Å / Origin y: 29.1551 Å / Origin z: -1.3195 Å
111213212223313233
T0.1561 Å2-0.0152 Å20.0169 Å2-0.1923 Å20.0438 Å2--0.1876 Å2
L1.9306 °21.7164 °21.8834 °2-3.2477 °22.2088 °2--4.0038 °2
S-0.0088 Å °-0.0134 Å °-0.1105 Å °-0.0375 Å °0.033 Å °0.0462 Å °0.163 Å °-0.2247 Å °-0.0197 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 68
2X-RAY DIFFRACTION1allB8 - 70
3X-RAY DIFFRACTION1allA1 - 136

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