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- PDB-2iwp: 12th PDZ domain of Multiple PDZ Domain Protein MPDZ -

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Basic information

Entry
Database: PDB / ID: 2iwp
Title12th 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 / microtubule organizing center organization / apicolateral plasma membrane / bicellular tight junction / regulation of microtubule cytoskeleton organization / 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 / PDZ 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: 2.15 Å
AuthorsElkins, J.M. / Yang, X. / Gileadi, C. / Schoch, G. / Johansson, C. / Savitsky, P. / Berridge, G. / Smee, C.E.A. / Turnbull, A. / Pike, A. ...Elkins, J.M. / Yang, X. / Gileadi, C. / Schoch, G. / Johansson, C. / Savitsky, P. / Berridge, G. / Smee, C.E.A. / Turnbull, A. / Pike, A. / 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 Extension.
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 26, 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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MULTIPLE PDZ DOMAIN PROTEIN
B: MULTIPLE PDZ DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,1012
Polymers25,1012
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-36.3 kcal/mol
Surface area11250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)76.710, 88.099, 73.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1808 - 1854
2114B1808 - 1854
1214A1860 - 1868
2214B1860 - 1868
1314A1871 - 1917
2314B1871 - 1917
1121A1924 - 1927
2121B1924 - 1927

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.99871, -0.03148, -0.03987), (0.00024, 0.78183, -0.62349), (0.0508, -0.6227, -0.78081)
Vector: 53.44674, 9.43359, 12.09089)
DetailsBIOLOGICAL ASSEMBLY: MONOMERIC

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Components

#1: Protein MULTIPLE PDZ DOMAIN PROTEIN


Mass: 12550.251 Da / Num. of mol.: 2 / Fragment: 12TH PDZ DOMAIN, RESIDUES 1831-1923
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 / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.46 Å3/Da / Density % sol: 50.1 % / Description: NONE
Crystal growpH: 4.5 / Details: 50% PEG 300, 0.2M LI2SO4, 0.1M ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.15→57.83 Å / Num. obs: 13731 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % 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 2FNE

2fne


Resolution: 2.15→57.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 12.001 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 687 5 %RANDOM
Rwork0.221 ---
obs0.223 13033 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--3.14 Å20 Å2
3----3.4 Å2
Refinement stepCycle: LAST / Resolution: 2.15→57.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 0 0 24 1401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221389
X-RAY DIFFRACTIONr_bond_other_d0.0010.02870
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9721884
X-RAY DIFFRACTIONr_angle_other_deg0.91932163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9225.38539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47415226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.274155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_nbd_refined0.2090.2275
X-RAY DIFFRACTIONr_nbd_other0.2070.2883
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2706
X-RAY DIFFRACTIONr_nbtor_other0.0930.2815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9091.5994
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39921554
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1943427
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5454.5330
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

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
246tight positional0.060.05
1843medium positional0.480.5
246tight thermal0.310.5
1843medium thermal1.142
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 51
Rwork0.251 944
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)
13.9561-0.176-2.78890.31010.051911.7807-0.1916-0.5656-0.19150.0166-0.10390.09470.5360.660.2955-0.29610.05310.0277-0.13950.0193-0.136918.28417.06111.162
26.15890.24350.04521.5458-1.12986.8801-0.16-0.5251-0.7480.11970.0123-0.16230.47110.32130.1477-0.33090.01940.0046-0.0230.0351-0.16335.99315.748-5.527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1808 - 1917
2X-RAY DIFFRACTION1B1924 - 1927
3X-RAY DIFFRACTION2B1808 - 1917
4X-RAY DIFFRACTION2A1924 - 1927

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