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

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Basic information

Entry
Database: PDB / ID: 2iwo
Title12th PDZ domain of Multiple PDZ Domain Protein MPDZ
ComponentsMULTIPLE PDZ DOMAIN PROTEIN
KeywordsSIGNALING PROTEIN / SGC / MUPP1 / MUPP-1 / PDZ DOMAIN / HOST-VIRUS INTERACTION / STRUCTURAL GENOMICS CONSORTIUM / SYNAPTOSOME / TIGHT JUNCTION / ALTERNATIVE SPLICING
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: 1.7 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 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 26, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / 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
Water2,054114
1
A: MULTIPLE PDZ DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,5501
Polymers12,5501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MULTIPLE PDZ DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,5501
Polymers12,5501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-12.2 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.483, 76.403, 32.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1808 - 1839
2114B1808 - 1839
1214A1844 - 1852
2214B1844 - 1852
1314A1860 - 1867
2314B1860 - 1867
1414A1876 - 1917
2414B1876 - 1917

NCS oper: (Code: given
Matrix: (0.72219, -0.10791, -0.68323), (-0.12442, -0.99191, 0.02515), (-0.68042, 0.06685, -0.72977)
Vector: 17.98562, 62.46926, 35.07616)
DetailsBIOLOGICAL ASSEMBLY: MONOMERIC IN SOLUTION

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Components

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


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) / Variant (production host): R3 ROSETTA / References: UniProt: O75970
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.85 Å3/Da / Density % sol: 33.6 %
Crystal growpH: 7.5 / Details: 2M (NH4)2SO4, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8983
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8983 Å / Relative weight: 1
ReflectionResolution: 1.7→38.21 Å / Num. obs: 21145 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / % 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: 1.7→53.3 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.929 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1082 5.1 %RANDOM
Rwork0.183 ---
obs0.184 20020 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→53.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 0 114 1458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221355
X-RAY DIFFRACTIONr_bond_other_d0.0010.02859
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9731834
X-RAY DIFFRACTIONr_angle_other_deg0.92132134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41325.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89315227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.81155
X-RAY DIFFRACTIONr_chiral_restr0.0950.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
X-RAY DIFFRACTIONr_nbd_refined0.1990.2232
X-RAY DIFFRACTIONr_nbd_other0.2010.2831
X-RAY DIFFRACTIONr_nbtor_refined0.170.2676
X-RAY DIFFRACTIONr_nbtor_other0.0870.2750
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3723958
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.99351504
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.0477429
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.38811330
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 / Ens-ID: 1 / Number: 748 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.440.5
medium thermal22
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 94
Rwork0.222 1423

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