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- PDB-4r2z: Molecular Analysis of the PDZ4 Domain of Mouse PDZK1 -

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Basic information

Entry
Database: PDB / ID: 4r2z
TitleMolecular Analysis of the PDZ4 Domain of Mouse PDZK1
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF3
KeywordsTRANSPORT PROTEIN / PDZ domain / Adaptor protein
Function / homology
Function and homology information


scavenger receptor binding / microvillus membrane / brush border / positive regulation of protein targeting to membrane / transporter activator activity / protein-membrane adaptor activity / regulation of monoatomic anion transport / protein localization to plasma membrane / PDZ domain binding / brush border membrane ...scavenger receptor binding / microvillus membrane / brush border / positive regulation of protein targeting to membrane / transporter activator activity / protein-membrane adaptor activity / regulation of monoatomic anion transport / protein localization to plasma membrane / PDZ domain binding / 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
Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBirrane, G. / Kocher, O. / Krieger, M.
CitationJournal: To be Published
Title: Molecular Analysis of the PDZ4 domain from Mouse PDZK1
Authors: Birrane, G. / Kocher, O. / Krieger, M.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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


Theoretical massNumber of molelcules
Total (without water)20,2675
Polymers19,9622
Non-polymers3043
Water2,288127
1
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1933
Polymers9,9811
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0732
Polymers9,9811
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.256, 89.214, 33.809
Angle α, β, γ (deg.)90.00, 113.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: 9981.234 Da / Num. of mol.: 2 / Fragment: PDZ4 domain, UNP residues 375-459
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdzk1, Cap70, Nherf3 / Plasmid: pGEX4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9JIL4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.15M Potassium Bromide, 24% PEGMME 2000, 15% Ethylene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2014
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: 1.6→100 Å / Num. all: 22402 / Num. obs: 22402 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 %
Reflection shellResolution: 1.6→1.66 Å / % possible all: 51.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.61 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.115 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 930 5 %RANDOM
Rwork0.18689 ---
obs0.18867 17532 98.61 %-
all-20134 --
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: 38.846 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å20.26 Å2
2---0.69 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 20 127 1409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191331
X-RAY DIFFRACTIONr_bond_other_d0.0010.021283
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9771792
X-RAY DIFFRACTIONr_angle_other_deg0.84732964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2635171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.49525.15266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39615233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.019159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
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_it2.2962.365669
X-RAY DIFFRACTIONr_mcbond_other2.132.363668
X-RAY DIFFRACTIONr_mcangle_it3.2933.523836
X-RAY DIFFRACTIONr_mcangle_other2.9612.211840
X-RAY DIFFRACTIONr_scbond_it3.5742.92662
X-RAY DIFFRACTIONr_scbond_other2.6721.869642
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0182.664935
X-RAY DIFFRACTIONr_long_range_B_refined8.44213.6421493
X-RAY DIFFRACTIONr_long_range_B_other8.48713.0861458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 77 -
Rwork0.292 1118 -
obs--87.8 %
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)
11.7067-0.2986-0.92824.3710.04871.15890.0343-0.03890.13320.0082-0.02240.0282-0.0365-0.0053-0.01190.08120.00770.04770.0081-0.02380.142617.67428.50723.719
20.33050.30970.03514.2247-0.95261.43860.03350.0323-0.0031-0.01290.06320.1880.10340.0084-0.09670.10870.00990.09110.0076-0.01020.184918.62552.37720.572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A374 - 457
2X-RAY DIFFRACTION2B376 - 456

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