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- PDB-2qg1: Crystal structure of the 11th PDZ domain of MPDZ (MUPP1) -

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Basic information

Entry
Database: PDB / ID: 2qg1
TitleCrystal structure of the 11th PDZ domain of MPDZ (MUPP1)
ComponentsMultiple PDZ domain protein
KeywordsSIGNALING PROTEIN / MPDZ / MUPP1 / Structural Genomics / Structural Genomics Consortium / SGC
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: 1.4 Å
AuthorsPapagrigoriou, E. / Salah, E. / Phillips, C. / Savitsky, P. / Boisguerin, P. / Oschkinat, H. / Gileadi, C. / Yang, X. / Elkins, J.M. / Ugochukwu, E. ...Papagrigoriou, E. / Salah, E. / Phillips, C. / Savitsky, P. / Boisguerin, P. / Oschkinat, H. / Gileadi, C. / Yang, X. / Elkins, J.M. / Ugochukwu, E. / Bunkoczi, G. / Uppenberg, J. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the 11th PDZ domain of MPDZ (MUPP1).
Authors: Papagrigoriou, E. / Salah, E. / Phillips, C. / Savitsky, P. / Boisguerin, P. / Oschkinat, H. / Gileadi, C. / Yang, X. / Elkins, J.M. / Ugochukwu, E. / Bunkoczi, G. / Uppenberg, J. / Doyle, D.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multiple PDZ domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6983
Polymers9,5741
Non-polymers1242
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.409, 36.919, 63.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Multiple PDZ domain protein / Multi-PDZ domain protein 1 / MPDZ


Mass: 9574.009 Da / Num. of mol.: 1 / Fragment: 11th PDZ domain / Mutation: E1727G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPDZ, MUPP1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: O75970
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9182 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9182 Å / Relative weight: 1
ReflectionResolution: 1.4→31.8 Å / Num. all: 15501 / Num. obs: 15501 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 13.5
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8319 / Rsym value: 0.394 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2HE2, 1TP3

2he2

1tp3


Resolution: 1.4→31.8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.633 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23418 780 5 %RANDOM
Rwork0.16937 ---
all0.17252 14686 --
obs0.17252 14686 96.16 %-
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: 14.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---1.84 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.4→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms667 0 16 121 804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022687
X-RAY DIFFRACTIONr_bond_other_d0.0010.02472
X-RAY DIFFRACTIONr_angle_refined_deg1.4892.003927
X-RAY DIFFRACTIONr_angle_other_deg0.86531167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7245100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5142524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6915127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.867155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02122
X-RAY DIFFRACTIONr_nbd_refined0.2080.2123
X-RAY DIFFRACTIONr_nbd_other0.1940.2491
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2320
X-RAY DIFFRACTIONr_nbtor_other0.090.2407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.222
X-RAY DIFFRACTIONr_mcbond_it5.5575483
X-RAY DIFFRACTIONr_mcbond_other3.8475195
X-RAY DIFFRACTIONr_mcangle_it6.3597727
X-RAY DIFFRACTIONr_scbond_it7.7929244
X-RAY DIFFRACTIONr_scangle_it9.26111194
X-RAY DIFFRACTIONr_rigid_bond_restr4.20531226
X-RAY DIFFRACTIONr_sphericity_free12.9683121
X-RAY DIFFRACTIONr_sphericity_bonded6.72331155
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 45 -
Rwork0.212 1047 -
obs--94.46 %

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