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- PDB-3r68: Molecular Analysis of the PDZ3 domain of PDZK1 -

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Basic information

Entry
Database: PDB / ID: 3r68
TitleMolecular Analysis of the PDZ3 domain of PDZK1
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF3
KeywordsSIGNALING PROTEIN / PDZ domain / adaptor protein / SR-BI
Function / homology
Function and homology information


scavenger receptor binding / microvillus membrane / positive regulation of protein targeting to membrane / protein-membrane adaptor activity / regulation of monoatomic anion transport / protein localization to plasma membrane / brush border membrane / in utero embryonic development / apical plasma membrane / signaling receptor binding ...scavenger receptor binding / microvillus membrane / positive regulation of protein targeting to membrane / protein-membrane adaptor activity / regulation of monoatomic anion transport / protein localization to plasma membrane / brush border membrane / in utero embryonic development / apical plasma membrane / signaling receptor binding / protein-containing complex binding / plasma membrane
Similarity search - Function
: / 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
ACETATE ION / Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsKocher, O. / Birrane, G. / Krieger, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Identification of the PDZ3 Domain of the Adaptor Protein PDZK1 as a Second, Physiologically Functional Binding Site for the C Terminus of the High Density Lipoprotein Receptor Scavenger Receptor Class B Type I.
Authors: Kocher, O. / Birrane, G. / Yesilaltay, A. / Shechter, S. / Pal, R. / Daniels, K. / Krieger, M.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,94115
Polymers10,2421
Non-polymers69914
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
hetero molecules

A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,88230
Polymers20,4832
Non-polymers1,39828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4870 Å2
ΔGint-412 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.910, 69.910, 37.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-309-

ARG

21A-109-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF3 / NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi ...NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi cotransporter C-terminal-associated protein 1 / NaPi-Cap1 / PDZ domain-containing protein 1 / Sodium-hydrogen exchanger regulatory factor 3


Mass: 10241.570 Da / Num. of mol.: 1 / Fragment: PDZ3 (UNP Residues 237-323)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cap70, Nherf3, Pdzk1 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9JIL4

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Non-polymers , 6 types, 130 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2M Zinc acetate, 0.1M sodium cacodylate, pH 6.2, 15% (W/V) PEG 3350, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 21, 2010 / Details: mirrors
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. all: 28919 / Num. obs: 28919 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.2→1.22 Å / Rsym value: 0.069 / % possible all: 69.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.3→33.15 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.88 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.041 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15686 1162 5 %RANDOM
Rwork0.13071 ---
all0.13192 22255 --
obs0.13192 22255 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.561 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 23 116 771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022726
X-RAY DIFFRACTIONr_bond_other_d0.0010.02513
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.992986
X-RAY DIFFRACTIONr_angle_other_deg1.12931270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18124.84833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79715140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.88156
X-RAY DIFFRACTIONr_chiral_restr0.090.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021827
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02131
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.81.5458
X-RAY DIFFRACTIONr_mcbond_other0.5391.5188
X-RAY DIFFRACTIONr_mcangle_it2.6462739
X-RAY DIFFRACTIONr_scbond_it3.3833268
X-RAY DIFFRACTIONr_scangle_it5.2474.5237
X-RAY DIFFRACTIONr_rigid_bond_restr1.44931239
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.169 86 -
Rwork0.137 1592 -
obs--99.76 %

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