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- PDB-2fcf: The crystal structure of the 7th PDZ domain of MPDZ (MUPP-1) -

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Basic information

Entry
Database: PDB / ID: 2fcf
TitleThe crystal structure of the 7th PDZ domain of MPDZ (MUPP-1)
ComponentsMultiple PDZ domain protein
KeywordsSTRUCTURAL PROTEIN / Adaptor molecule / Protein linker / Structural Genomics / Structural Genomics Consortium / SGC
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 / Multiple PDZ domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)11,2701
Polymers11,2701
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.122, 43.801, 50.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer

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Components

#1: Protein Multiple PDZ domain protein / Multi PDZ domain protein 1 / Multi-PDZ-domain protein 1 / MPDZ / MUPP1


Mass: 11269.983 Da / Num. of mol.: 1 / Fragment: PDZ 7 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPDZ, MUPP1 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5VZ62, UniProt: O75970*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 41.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 30% mPEG 2K, 0.10M KSCN, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9001 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9001 Å / Relative weight: 1
ReflectionResolution: 1.76→32.99 Å / Num. all: 9475 / Num. obs: 8968 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.84 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073
Reflection shellResolution: 1.76→1.85 Å / Redundancy: 6.35 % / Rmerge(I) obs: 0.0955 / Mean I/σ(I) obs: 9.57 / Num. unique all: 1354 / Rsym value: 0.184 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n7f

1n7f


Resolution: 1.76→32.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.788 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24396 462 4.9 %RANDOM
Rwork0.20767 ---
all0.20937 9475 --
obs0.20937 8968 95.58 %-
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: 39.847 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2--3.36 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.76→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 0 0 39 702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022676
X-RAY DIFFRACTIONr_bond_other_d0.0010.02472
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.976912
X-RAY DIFFRACTIONr_angle_other_deg0.87731149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.387588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.48122.69226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5615118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.785157
X-RAY DIFFRACTIONr_chiral_restr0.090.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02129
X-RAY DIFFRACTIONr_nbd_refined0.210.291
X-RAY DIFFRACTIONr_nbd_other0.2060.2441
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2308
X-RAY DIFFRACTIONr_nbtor_other0.0860.2391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0670.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1243458
X-RAY DIFFRACTIONr_mcbond_other0.8153182
X-RAY DIFFRACTIONr_mcangle_it3.875708
X-RAY DIFFRACTIONr_scbond_it5.3217246
X-RAY DIFFRACTIONr_scangle_it7.73711203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 28 -
Rwork0.228 677 -
obs--99.72 %
Refinement TLS params.Method: refined / Origin x: 5.454 Å / Origin y: 4.2112 Å / Origin z: 1.9206 Å
111213212223313233
T-0.1648 Å20.0373 Å2-0.0095 Å2--0.1714 Å2-0.0507 Å2---0.16 Å2
L5.0405 °2-1.2414 °20.2255 °2-2.8921 °20.9072 °2--3.6947 °2
S-0.0499 Å °-0.1274 Å °-0.2486 Å °0.0682 Å °0.0211 Å °0.1735 Å °0.3387 Å °-0.0135 Å °0.0288 Å °

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