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- PDB-2fne: The crystal structure of the 13th PDZ domain of MPDZ -

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Basic information

Entry
Database: PDB / ID: 2fne
TitleThe crystal structure of the 13th PDZ domain of MPDZ
ComponentsMultiple PDZ domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Protein / SGC / Structural Genomics Consortium
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 / Multiple PDZ domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsPapagrigoriou, E. / Berridge, G. / Johansson, C. / Colebrook, S. / Salah, E. / Burgess, N. / Smee, C. / Savitsky, P. / Bray, J. / Schoch, G. ...Papagrigoriou, E. / Berridge, G. / Johansson, C. / Colebrook, S. / Salah, E. / Burgess, N. / Smee, C. / Savitsky, P. / Bray, J. / Schoch, G. / Phillips, C. / Gileadi, C. / Soundarajan, M. / Yang, X. / Elkins, J.M. / Gorrec, F. / Turnbull, A. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
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
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multiple PDZ domain protein
B: Multiple PDZ domain protein
C: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)37,5873
Polymers37,5873
Non-polymers00
Water3,585199
1
A: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)12,5291
Polymers12,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)12,5291
Polymers12,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)12,5291
Polymers12,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Multiple PDZ domain protein

C: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)25,0582
Polymers25,0582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_547-x,y-1/2,-z+21
Buried area1010 Å2
ΔGint-11 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.943, 62.380, 53.128
Angle α, β, γ (deg.)90.00, 106.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 1956 - 2048 / Label seq-ID: 25 - 117

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsEach of the three monomers found in the asu represents a biological unit

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Components

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


Mass: 12529.081 Da / Num. of mol.: 3 / Fragment: MPDZ domain, residues 1955-2042
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): BL-21(DE3)R3 / References: UniProt: Q5VZ62, UniProt: O75970*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 8% PEG P3350, 0.1M acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.83→39.5 Å / Num. all: 26633 / Num. obs: 26605 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0508
Reflection shellResolution: 1.83→1.95 Å / Rmerge(I) obs: 0.4753 / Mean I/σ(I) obs: 2.15 / Num. unique all: 4556 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2byg

2byg


Resolution: 1.83→39.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.208 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24293 2038 7.7 %RANDOM
Rwork0.19016 ---
all0.19415 26633 --
obs0.19415 26605 99.97 %-
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: 44.104 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.06 Å2
2--0.05 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.83→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 0 199 2374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9832995
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36624.55779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27215364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5741512
X-RAY DIFFRACTIONr_chiral_restr0.1190.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021646
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2877
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21520
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.27231517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.24352369
X-RAY DIFFRACTIONr_scbond_it5.9517759
X-RAY DIFFRACTIONr_scangle_it8.01611622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 636 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.340.5
2Bmedium positional0.610.5
3Cmedium positional0.530.5
1Amedium thermal2.82
2Bmedium thermal1.982
3Cmedium thermal2.022
LS refinement shellResolution: 1.83→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 141 -
Rwork0.237 1799 -
obs--100 %

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