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- PDB-4cn0: An intertwined homodimer of the PDZ homology domain of AHNAK2 -

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Basic information

Entry
Database: PDB / ID: 4cn0
TitleAn intertwined homodimer of the PDZ homology domain of AHNAK2
ComponentsPROTEIN AHNAK2
KeywordsCELL CYCLE / DOMAIN SWAPPING / INTERTWINING / PDZ DOMAIN
Function / homology
Function and homology information


costamere / regulation of RNA splicing / T-tubule / cytoplasmic vesicle membrane / sarcolemma / Z disc / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHan, H. / Kursula, P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Periaxin and Ahnak Nucleoprotein 2 Form Intertwined Homodimers Through Domain Swapping
Authors: Han, H. / Kursula, P.
History
DepositionJan 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Atomic model
Revision 1.3Aug 27, 2014Group: Database references
Revision 1.4Dec 17, 2014Group: Data collection
Revision 1.5Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PROTEIN AHNAK2
B: PROTEIN AHNAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2786
Polymers21,6562
Non-polymers6224
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-27.7 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.730, 81.730, 65.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2067-

HOH

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Components

#1: Protein PROTEIN AHNAK2


Mass: 10828.055 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 108-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q8IVF2
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.91 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growpH: 7.5 / Details: 10% PEG8000, 50 MM KH2PO4, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9669
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9669 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 25792 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 18.7 % / Biso Wilson estimate: 36.79 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CMZ

4cmz


Resolution: 1.75→47.999 Å / SU ML: 0.15 / σ(F): 1.37 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 1288 5 %
Rwork0.1805 --
obs0.1818 25739 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→47.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 40 113 1576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071505
X-RAY DIFFRACTIONf_angle_d1.1052020
X-RAY DIFFRACTIONf_dihedral_angle_d16.718584
X-RAY DIFFRACTIONf_chiral_restr0.037223
X-RAY DIFFRACTIONf_plane_restr0.009258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.2821400.26012660X-RAY DIFFRACTION100
1.82-1.90290.25411430.23382696X-RAY DIFFRACTION100
1.9029-2.00320.26271400.21122671X-RAY DIFFRACTION100
2.0032-2.12870.22471420.18522676X-RAY DIFFRACTION100
2.1287-2.29310.23831420.18082708X-RAY DIFFRACTION100
2.2931-2.52380.20151430.18372710X-RAY DIFFRACTION100
2.5238-2.8890.23681430.18622729X-RAY DIFFRACTION100
2.889-3.63960.20341450.18142754X-RAY DIFFRACTION100
3.6396-48.01670.1831500.16882847X-RAY DIFFRACTION100
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)
10.5954-0.3206-0.50630.48090.14230.6205-0.17350.161-0.08-0.17980.21420.21880.61380.14960.00030.6301-0.0008-0.04290.33880.01360.409336.05018.1187-6.7701
20.3621-0.4533-0.39070.70050.05270.95230.50450.27460.02330.1757-0.25880.16430.7119-0.44930.00020.3851-0.0829-0.04170.41250.00210.388628.286317.9932-13.5364
30.4381-0.3981-0.39381.06160.42510.6328-0.29880.2486-0.0533-0.00650.0795-0.46930.12960.4942-0.00030.3470.00460.00530.3850.03380.446241.551318.7305-10.927
41.2183-0.41020.06431.1266-0.02710.2046-0.1427-0.17640.0882-0.18560.18640.02470.1192-0.0895-0.00020.3753-0.0232-0.00390.36370.02370.392331.472917.0997-0.8168
51.86410.2652-2.04830.6216-0.23012.2559-0.186-0.02850.08830.30070.30690.01380.1734-0.5086-0.00090.37490.0441-0.00570.56890.08690.421722.082718.47377.4579
60.2967-0.3254-0.2370.46320.01670.342-0.2747-0.8844-0.5170.28570.4013-0.23190.8306-0.67970.00010.63160.029-0.02870.63810.11120.573123.49757.876612.7336
70.15980.32930.25383.0488-0.89461.08010.24740.42470.10130.90550.70860.56160.0408-0.55190.19840.27540.0960.01340.83730.18550.453316.641720.71689.6185
82.89370.11020.13772.32270.93611.7103-0.74850.3291-0.48060.18290.8866-0.0321-0.6859-0.09430.00780.50380.15460.0260.63170.13460.368718.767621.498715.2799
90.1065-0.1462-0.02850.35110.1050.03770.0847-1.0067-1.3146-0.11790.64940.10120.9323-0.83990.01610.5239-0.02110.10240.95160.2520.698713.688211.697611.6815
101.7916-1.02-1.23732.1713-0.56292.3082-0.1521-0.06720.06930.08450.22960.0740.0007-0.36280.00010.2934-0.0228-0.02870.39170.04320.37625.447719.6379-0.1858
110.91420.0078-0.28170.26550.15440.2193-0.17470.1414-0.28140.07710.0261-0.06811.35530.2228-0.00010.60730.06070.02670.3475-0.04210.403434.25828.5152-9.545
120.17590.0707-0.0580.31460.06180.06820.2758-0.48570.76440.081-0.7421.3616-1.5103-0.6749-0.00660.7126-0.00140.0620.54-0.14830.512842.5388-9.7383-28.4079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 109 THROUGH 123 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 124 THROUGH 138 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 139 THROUGH 154 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 155 THROUGH 170 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 171 THROUGH 195 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 111 THROUGH 120 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 121 THROUGH 130 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 131 THROUGH 145 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 146 THROUGH 154 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 155 THROUGH 185 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 186 THROUGH 195 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 196 THROUGH 203 )

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