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- PDB-8ah7: Crystal Structure of the third PDZ domain of PSD-95 protein in th... -

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Basic information

Entry
Database: PDB / ID: 8ah7
TitleCrystal Structure of the third PDZ domain of PSD-95 protein in the space group P212121 at pH 4.0
ComponentscDNA FLJ50577, highly similar to Discs large homolog 4
KeywordsPROTEIN BINDING / PDZ domain
Function / homology
Function and homology information


neuromuscular junction / kinase binding / chemical synaptic transmission / neuron projection
Similarity search - Function
PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
cDNA FLJ50577, highly similar to Discs large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
Model detailspH 4.0 P3112 polymorph
AuthorsCamara-Artigas, A. / Salinas-Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other governmentUAL-FEDER-UAL18-BIO-B005-B Spain
CitationJournal: Crystals / Year: 2023
Title: pH-Driven Polymorphic Behaviour of the Third PDZ Domain of PSD95: The Role of Electrostatic Interactions
Authors: Salinas-Garcia, M.C. / Plaza-Garrido, M. / Gavira, J.A. / Murciano-Calles, J. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Martinez, J.C. / Camara-Artigas, A.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: cDNA FLJ50577, highly similar to Discs large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2452
Polymers11,1481
Non-polymers961
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.562, 36.747, 73.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cDNA FLJ50577, highly similar to Discs large homolog 4


Mass: 11148.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7Z4H2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 30% PEG 4000, 0.2M Ammonium Sulfate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.25→19.53 Å / Num. obs: 24458 / % possible obs: 98.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.023 / Rrim(I) all: 0.05 / Net I/σ(I): 8.2 / Num. measured all: 99957 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.25-1.274.10.883499912050.7620.4651.005199.6
6.85-19.533.60.0415521520.9950.0220.04724.286.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QJI

6qji


Resolution: 1.25→19.53 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 1248 5.12 %
Rwork0.1606 23127 -
obs0.1625 24375 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.23 Å2 / Biso mean: 27.3931 Å2 / Biso min: 13.82 Å2
Refinement stepCycle: final / Resolution: 1.25→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms764 0 5 117 886
Biso mean--37.27 33.37 -
Num. residues----102
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.30.32021220.29432574269699
1.3-1.360.33741420.25032596273899
1.36-1.430.29871330.22762532266599
1.43-1.520.2611480.18052548269698
1.52-1.640.20331400.15492582272298
1.64-1.80.21881450.14422568271398
1.8-2.060.19351350.13972556269197
2.06-2.60.18481500.1542574272497
2.6-19.530.17341330.15342597273092

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