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- PDB-2z17: Crystal structure of PDZ domain from human Pleckstrin homology, Sec7 -

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Basic information

Entry
Database: PDB / ID: 2z17
TitleCrystal structure of PDZ domain from human Pleckstrin homology, Sec7
ComponentsPleckstrin homology Sec7 and coiled-coil domains-binding protein
KeywordsPROTEIN BINDING / PDZ domain / Coiled coil / Cytoplasm / Membrane / Polymorphism / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of cell adhesion / cell cortex / early endosome / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
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
Cytohesin-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PDZ domain from human Pleckstrin homology, Sec7
Authors: Kishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 9, 2020Group: Database references / Structure summary / Category: citation / struct / struct_ref_seq_dif
Item: _citation.title / _struct.title / _struct_ref_seq_dif.details
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleckstrin homology Sec7 and coiled-coil domains-binding protein


Theoretical massNumber of molelcules
Total (without water)11,3041
Polymers11,3041
Non-polymers00
Water19811
1
A: Pleckstrin homology Sec7 and coiled-coil domains-binding protein

A: Pleckstrin homology Sec7 and coiled-coil domains-binding protein


Theoretical massNumber of molelcules
Total (without water)22,6092
Polymers22,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area1920 Å2
ΔGint-12 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.917, 65.917, 81.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-111-

HOH

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Components

#1: Protein Pleckstrin homology Sec7 and coiled-coil domains-binding protein / Cytohesin-binding protein HE / CYBR / Cytohesin binder and regulator / Cytohesin-interacting protein


Mass: 11304.448 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PK060110-70 / Production host: Cell-free protein synthesis / References: UniProt: O60759
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na, 2.0M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9789, 0.9794, 0.964
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2006 / Details: mirrors
RadiationMonochromator: Si II / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97941
30.9641
ReflectionResolution: 2.5→50 Å / Num. obs: 3931 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 19.5 % / Biso Wilson estimate: 38.2 Å2 / Rsym value: 0.061 / Net I/σ(I): 41.9
Reflection shellResolution: 2.5→2.63 Å / Mean I/σ(I) obs: 15.6 / Rsym value: 0.232 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→28.54 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 145252.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.334 195 9.7 %RANDOM
Rwork0.244 ---
obs0.244 3931 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1437 Å2 / ksol: 0.340996 e/Å3
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å26.25 Å20 Å2
2---3.37 Å20 Å2
3---6.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 0 0 11 745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.07 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 31 3.4 %
Rwork0.304 868 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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