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- PDB-2v90: Crystal structure of the 3rd PDZ domain of intestine- and kidney-... -

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Basic information

Entry
Database: PDB / ID: 2v90
TitleCrystal structure of the 3rd PDZ domain of intestine- and kidney- enriched PDZ domain IKEPP (PDZD3)
ComponentsPDZ DOMAIN-CONTAINING PROTEIN 3
KeywordsPROTEIN BINDING / PDZD3 / MEMBRANE / PDZ DOMAIN / PROTEIN-BINDING
Function / homology
Function and homology information


guanylate cyclase inhibitor activity / Intestinal infectious diseases / receptor guanylyl cyclase signaling pathway / water transport / negative regulation of receptor guanylyl cyclase signaling pathway / apical junction complex / ion channel inhibitor activity / ubiquitin-specific protease binding / brush border / protein-membrane adaptor activity ...guanylate cyclase inhibitor activity / Intestinal infectious diseases / receptor guanylyl cyclase signaling pathway / water transport / negative regulation of receptor guanylyl cyclase signaling pathway / apical junction complex / ion channel inhibitor activity / ubiquitin-specific protease binding / brush border / protein-membrane adaptor activity / monoatomic ion transport / protein localization to plasma membrane / response to toxic substance / apical part of cell / apical plasma membrane / signaling receptor binding / plasma membrane / cytosol
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-RF4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUppenberg, J. / Gileadi, C. / Phillips, C. / Elkins, J. / Bunkoczi, G. / Cooper, C. / Pike, A.C.W. / Salah, E. / Ugochukwu, E. / Arrowsmith, C.H. ...Uppenberg, J. / Gileadi, C. / Phillips, C. / Elkins, J. / Bunkoczi, G. / Cooper, C. / Pike, A.C.W. / Salah, E. / Ugochukwu, E. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Doyle, D.A.
CitationJournal: To be Published
Title: Crystal Structure of the 3Rd Pdz Domain of Intestine- and Kidney-Enriched Pdz Domain Ikepp (Pdzd3)
Authors: Uppenberg, J. / Gileadi, C. / Phillips, C. / Elkins, J. / Bunkoczi, G. / Cooper, C. / Pike, A.C.W. / Salah, E. / Ugochukwu, E. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Doyle, D.A.
History
DepositionAug 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PDZ DOMAIN-CONTAINING PROTEIN 3
B: PDZ DOMAIN-CONTAINING PROTEIN 3
C: PDZ DOMAIN-CONTAINING PROTEIN 3
D: PDZ DOMAIN-CONTAINING PROTEIN 3
E: PDZ DOMAIN-CONTAINING PROTEIN 3
F: PDZ DOMAIN-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8349
Polymers61,5456
Non-polymers2883
Water6,990388
1
A: PDZ DOMAIN-CONTAINING PROTEIN 3
C: PDZ DOMAIN-CONTAINING PROTEIN 3
E: PDZ DOMAIN-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8694
Polymers30,7733
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PDZ DOMAIN-CONTAINING PROTEIN 3
D: PDZ DOMAIN-CONTAINING PROTEIN 3
F: PDZ DOMAIN-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9655
Polymers30,7733
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.150, 97.950, 59.500
Angle α, β, γ (deg.)90.00, 99.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A244 - 267
2115B244 - 267
3115C244 - 267
4115D244 - 267
5115E244 - 267
6115F244 - 267
1215A275 - 299
2215B275 - 299
3215C275 - 299
4215D275 - 299
5215E275 - 299
6215F275 - 299
1315A300 - 332
2315B300 - 332
3315C300 - 332
4315D300 - 332
5315E300 - 332
6315F300 - 332

NCS oper:
IDCodeMatrixVector
1given(0.99996, -0.00619, 0.00578), (0.00632, 0.99972, -0.02263), (-0.00564, 0.02266, 0.99973)19.25825, 48.58855, 30.25384
2given(-0.99996, 0.0079, -0.00499), (0.00035, -0.50209, -0.86482), (-0.00933, -0.86478, 0.50206)29.15355, -51.12002, -29.03732
3given(-0.99977, 0.0197, -0.008), (-0.00293, -0.50012, -0.86595), (-0.02106, -0.86573, 0.50006)48.38662, -2.11191, 0.71022
4given(0.99994, -0.0072, 0.00877), (-0.01131, -0.57358, 0.81907), (-0.00087, -0.81912, -0.57362)0.2344, -28.58708, -43.79194
5given(0.99996, -0.00392, 0.00802), (-0.00881, -0.57748, 0.81635), (0.00143, -0.81639, -0.5775)19.1838, 20.06012, -14.01673

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Components

#1: Protein
PDZ DOMAIN-CONTAINING PROTEIN 3 / PDZ DOMAIN-CONTAINING PROTEIN 2 / INTESTINAL AND KIDNEY-ENRICHED PDZ PROTEIN / INTESTINE- AND ...PDZ DOMAIN-CONTAINING PROTEIN 2 / INTESTINAL AND KIDNEY-ENRICHED PDZ PROTEIN / INTESTINE- AND KIDNEY-ENRICHED PDZ DOMAIN IKEPP


Mass: 10257.568 Da / Num. of mol.: 6 / Fragment: PDZ DOMAIN, RESIDUES 246-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q86UT5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE LAST 4 RESIDUES (GLU336-VAL339) IS A COMMON PDZ-BINDING SEQUENCE ENGINEERED AT THE C-TERMINUS ...THE LAST 4 RESIDUES (GLU336-VAL339) IS A COMMON PDZ-BINDING SEQUENCE ENGINEERED AT THE C-TERMINUS OF THE PROTEIN TO PROMOTE MACROMOLECULAR CONTACTS. THE FIRST TWO RESIDUES BELONG TO A CLEAVED HIS-TAG LINKER

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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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 5.5 / Details: 2M (NH4)2SO4, 0.1M BIS-TRIS, PH=5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03315
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 16, 2007
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2→42.7 Å / Num. obs: 36079 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.7 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9O

1g9o


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.184 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1798 5 %RANDOM
Rwork0.193 ---
obs0.196 34206 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-0.59 Å2
2--0.19 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 15 388 4616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224320
X-RAY DIFFRACTIONr_bond_other_d0.0010.023042
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9925825
X-RAY DIFFRACTIONr_angle_other_deg0.92337415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0924.233189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85815738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.961536
X-RAY DIFFRACTIONr_chiral_restr0.0880.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.20.2720
X-RAY DIFFRACTIONr_nbd_other0.2020.23059
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21965
X-RAY DIFFRACTIONr_nbtor_other0.0840.22520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.27632885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.32454429
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.07881597
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.687111396
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A458medium positional0.220.5
2B458medium positional0.20
3C458medium positional0.170
4D458medium positional0.20
5E458medium positional0.240
6F458medium positional0.280
1A522loose positional0.525
2B522loose positional0.580.01
3C522loose positional0.40
4D522loose positional0.410
5E522loose positional0.510
6F522loose positional0.620
1A458medium thermal1.352
2B458medium thermal1.230
3C458medium thermal1.190
4D458medium thermal1.170
5E458medium thermal1.110
6F458medium thermal1.150
1A522loose thermal1.2310
2B522loose thermal1.150.02
3C522loose thermal1.260
4D522loose thermal1.160
5E522loose thermal1.190
6F522loose thermal1.120
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 109
Rwork0.212 2477
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)
13.4807-0.1868-0.29341.0563-0.27420.62070.1687-0.23040.05320.1656-0.0877-0.02340.0417-0.0337-0.0809-0.021-0.03060.0058-0.0803-0.0122-0.07025.2995-41.8697-9.6254
23.07060.3280.09241.13880.23391.20090.1567-0.25530.11950.2491-0.13930.04330.011-0.0693-0.0174-0.0122-0.02780.0207-0.068-0.0156-0.068324.76957.005219.6598
33.3846-0.5972-0.28441.50080.19920.7576-0.0078-0.08-0.37360.27090.0279-0.1230.14970.0288-0.0201-0.03860.0087-0.0177-0.05-0.0275-0.019223.7061-21.54261.95
43.3111-0.9149-0.51832.23050.85061.0788-0.0142-0.1475-0.29360.33360.0264-0.15960.14670.1002-0.01220.01290.0052-0.0304-0.0652-0.0088-0.058842.582727.295531.6913
52.7214-0.34780.95770.94870.16591.5781-0.01550.13380.0797-0.0223-0.08650.0371-0.0951-0.08240.1019-0.05190.02490.0076-0.0444-0.0379-0.05515.6602-12.6624-3.8867
63.222-0.31941.24040.85330.38971.43560.05950.19870.1127-0.0673-0.13460.0731-0.1336-0.08960.07510.02210.0325-0.0158-0.0174-0.0282-0.049324.43936.139125.7232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 339
2X-RAY DIFFRACTION2B244 - 339
3X-RAY DIFFRACTION3C244 - 339
4X-RAY DIFFRACTION4D244 - 339
5X-RAY DIFFRACTION5E244 - 339
6X-RAY DIFFRACTION6F244 - 339

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