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- PDB-2he4: The crystal structure of the second PDZ domain of human NHERF-2 (... -

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Basic information

Entry
Database: PDB / ID: 2he4
TitleThe crystal structure of the second PDZ domain of human NHERF-2 (SLC9A3R2) interacting with a mode 1 PDZ binding motif
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Phosphorylation / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


type 2 metabotropic glutamate receptor binding / type 3 metabotropic glutamate receptor binding / phosphatase binding / protein-membrane adaptor activity / endomembrane system / protein localization to plasma membrane / beta-catenin binding / protein-containing complex assembly / apical plasma membrane / cadherin binding ...type 2 metabotropic glutamate receptor binding / type 3 metabotropic glutamate receptor binding / phosphatase binding / protein-membrane adaptor activity / endomembrane system / protein localization to plasma membrane / beta-catenin binding / protein-containing complex assembly / apical plasma membrane / cadherin binding / signaling receptor binding / focal adhesion / extracellular exosome / identical protein binding / nucleus / plasma membrane
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPapagrigoriou, E. / Elkins, J.M. / Berridge, G. / Gileady, O. / Colebrook, S. / Gileadi, C. / Salah, E. / Savitsky, P. / Pantic, N. / Gorrec, F. ...Papagrigoriou, E. / Elkins, J.M. / Berridge, G. / Gileady, O. / Colebrook, S. / Gileadi, C. / Salah, E. / Savitsky, P. / Pantic, N. / Gorrec, F. / Bunkoczi, G. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions.
Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, P. / Doyle, D.A.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9932
Polymers9,9311
Non-polymers621
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.803, 37.677, 40.340
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-100-

HOH

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF2 / NHERF-2 / Tyrosine kinase activator protein 1 / TKA-1 / SRY-interacting protein 1 / SIP- 1 / Solute ...NHERF-2 / Tyrosine kinase activator protein 1 / TKA-1 / SRY-interacting protein 1 / SIP- 1 / Solute carrier family 9 isoform A3 regulatory factor 2 / NHE3 kinase A regulatory protein E3KARP / Sodium-hydrogen exchanger regulatory factor 2


Mass: 9931.314 Da / Num. of mol.: 1 / Fragment: PDZ 2 Domain (Residues 147-230) / Mutation: D229G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A3R2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 Rosetta / References: UniProt: Q15599
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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: 1.89 Å3/Da / Density % sol: 34.82 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97646 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 6, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97646 Å / Relative weight: 1
ReflectionResolution: 1.45→39.97 Å / Num. all: 13265 / Num. obs: 13060 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 0.98 % / Rmerge(I) obs: 0.0385
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 0.98 % / Rmerge(I) obs: 0.1403 / Mean I/σ(I) obs: 6.45 / Num. unique all: 2349 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i92 and 1g9o

1i92

1g9o


Resolution: 1.45→39.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.089 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18003 641 4.9 %RANDOM
Rwork0.12965 ---
all0.13203 13060 --
obs0.13203 12418 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.015 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å21.34 Å2
2---1.13 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms719 0 4 117 840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021733
X-RAY DIFFRACTIONr_bond_other_d0.0030.02553
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.988987
X-RAY DIFFRACTIONr_angle_other_deg0.95731330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.535589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10921.11136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.6215134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5761513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02154
X-RAY DIFFRACTIONr_nbd_refined0.2170.2107
X-RAY DIFFRACTIONr_nbd_other0.1970.2570
X-RAY DIFFRACTIONr_nbtor_refined0.160.2346
X-RAY DIFFRACTIONr_nbtor_other0.0820.2456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8163470
X-RAY DIFFRACTIONr_mcbond_other2.473182
X-RAY DIFFRACTIONr_mcangle_it4.6865732
X-RAY DIFFRACTIONr_scbond_it6.2738290
X-RAY DIFFRACTIONr_scangle_it8.62411255
X-RAY DIFFRACTIONr_rigid_bond_restr2.85131368
X-RAY DIFFRACTIONr_sphericity_free10.4183117
X-RAY DIFFRACTIONr_sphericity_bonded5.95431276
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 49 -
Rwork0.101 919 -
obs--98.17 %

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