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- PDB-2iwq: 7th PDZ domain of Multiple PDZ Domain Protein MPDZ -

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Basic information

Entry
Database: PDB / ID: 2iwq
Title7th PDZ domain of Multiple PDZ Domain Protein MPDZ
ComponentsMULTIPLE PDZ DOMAIN PROTEIN
KeywordsSIGNALING PROTEIN / SGC / PDZ / MPDZ / MUPP1 / MUPP- 1 / MEMBRANE / PDZ DOMAIN / HOST- VIRUS INTERACTION / STRUCTURAL GENOMICS CONSORTIUM / SYNAPTOSOME / TIGHT JUNCTION
Function / homology
Function and homology information


tight junction assembly / apicolateral plasma membrane / bicellular tight junction / apical part of cell / postsynaptic density / apical plasma membrane / dendrite / plasma membrane / cytoplasm
Similarity search - Function
Multiple PDZ domain protein / Unstructured region 10 on multiple PDZ protein / L27-2 / L27_2 / : / L27 domain / L27 domain profile. / L27 domain superfamily / PDZ domain / Pdz3 Domain ...Multiple PDZ domain protein / Unstructured region 10 on multiple PDZ protein / L27-2 / L27_2 / : / L27 domain / L27 domain profile. / L27 domain superfamily / 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
Multiple PDZ domain protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsElkins, J.M. / Berridge, G. / Savitsky, P. / Smee, C.E.A. / Turnbull, A. / Ugochukwu, E. / Papagrigoriou, E. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. ...Elkins, J.M. / Berridge, G. / Savitsky, P. / Smee, C.E.A. / Turnbull, A. / Ugochukwu, E. / Papagrigoriou, E. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Doyle, D.A.
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
DepositionJul 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MULTIPLE PDZ DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,6141
Polymers13,6141
Non-polymers00
Water61334
1
A: MULTIPLE PDZ DOMAIN PROTEIN

A: MULTIPLE PDZ DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,2272
Polymers27,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2480 Å2
ΔGint-17.16 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.370, 48.370, 75.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21A-2012-

HOH

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Components

#1: Protein MULTIPLE PDZ DOMAIN PROTEIN / MULTI-PDZ-DOMAIN PROTEIN 1 / MULTI PDZ DOMAIN PROTEIN 1


Mass: 13613.521 Da / Num. of mol.: 1 / Fragment: 7TH PDZ DOMAIN, RESIDUES 1148-1243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3ROSETTA / References: UniProt: O75970
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE LAST 4 RESIDUES (1244-1247) ARE A CLONING ARTEFACT

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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: 1.75 Å3/Da / Density % sol: 29.6 %
Crystal growpH: 8.5
Details: 0.2M NAF, 0.1M BISTRIS PROPANE PH8.5, 20% PEG3350, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→48.39 Å / Num. obs: 8738 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I92, 1G90

1i92

1g90


Resolution: 1.8→40.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.079 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 489 5.6 %RANDOM
Rwork0.201 ---
obs0.205 8204 98.7 %-
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: 38.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2--1.02 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms679 0 0 34 713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022697
X-RAY DIFFRACTIONr_bond_other_d0.0010.02480
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.971942
X-RAY DIFFRACTIONr_angle_other_deg0.88731174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.752592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18222.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.275156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02770
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02131
X-RAY DIFFRACTIONr_nbd_refined0.2130.2109
X-RAY DIFFRACTIONr_nbd_other0.190.2466
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2322
X-RAY DIFFRACTIONr_nbtor_other0.0880.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8593489
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.3845737
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.3667252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.01711204
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
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 43
Rwork0.243 576
Refinement TLS params.Method: refined / Origin x: 11.248 Å / Origin y: 4.743 Å / Origin z: 16.683 Å
111213212223313233
T-0.0418 Å2-0.0361 Å2-0.0254 Å2--0.1158 Å20.048 Å2---0.0332 Å2
L3.4686 °21.2491 °2-0.8264 °2-3.4225 °2-1.1976 °2--3.7064 °2
S0.0728 Å °0.228 Å °0.4448 Å °0.1645 Å °-0.0912 Å °-0.0207 Å °-0.372 Å °0.2514 Å °0.0184 Å °

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