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- PDB-1ihj: Crystal Structure of the N-terminal PDZ domain of InaD in complex... -

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Basic information

Entry
Database: PDB / ID: 1ihj
TitleCrystal Structure of the N-terminal PDZ domain of InaD in complex with a NorpA C-terminal peptide
Components
  • InaD
  • phospholipase C
KeywordsSIGNALING PROTEIN / intermolecular disulfide bond / PDZ domain
Function / homology
Function and homology information


myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of opsin-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / rhabdomere / cellular response to light stimulus / myosin binding / photoreceptor activity / phototransduction ...myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of opsin-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / rhabdomere / cellular response to light stimulus / myosin binding / photoreceptor activity / phototransduction / visual perception / sensory perception of sound / intracellular protein localization / signaling receptor complex adaptor activity / calmodulin binding
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
: / Inactivation-no-after-potential D protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKimple, M.E. / Siderovski, D.P. / Sondek, J.
CitationJournal: EMBO J. / Year: 2001
Title: Functional relevance of the disulfide-linked complex of the N-terminal PDZ domain of InaD with NorpA.
Authors: Kimple, M.E. / Siderovski, D.P. / Sondek, J.
History
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: InaD
B: InaD
C: phospholipase C
D: phospholipase C


Theoretical massNumber of molelcules
Total (without water)23,0554
Polymers23,0554
Non-polymers00
Water3,099172
1
A: InaD
D: phospholipase C


Theoretical massNumber of molelcules
Total (without water)11,5272
Polymers11,5272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-5 kcal/mol
Surface area5820 Å2
MethodPISA
2
B: InaD
C: phospholipase C


Theoretical massNumber of molelcules
Total (without water)11,5272
Polymers11,5272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-6 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.170, 44.150, 44.460
Angle α, β, γ (deg.)106.55, 100.61, 118.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein InaD


Mass: 10771.533 Da / Num. of mol.: 2 / Fragment: PDZ1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24008
#2: Protein/peptide phospholipase C / NorpA


Mass: 755.859 Da / Num. of mol.: 2 / Fragment: C-terminus / Source method: obtained synthetically
Details: This peptide was chemically synthesized. It consists of the final seven residues of phospholipase C (gktefca).
References: GenBank: 85099, phospholipase C
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, lithium sulfate, glycerol, dithiothreitol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
224 %PEG40001reservoir
3100 mMTris1reservoir
4200 mM1reservoirLiCl
510 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0072 Å / Relative weight: 1
ReflectionResolution: 1.76→20 Å / Num. all: 27241 / Num. obs: 25906 / % possible obs: 95.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.5
Reflection shellResolution: 1.76→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.156 / % possible all: 86.7
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 86.7 % / Num. unique obs: 2424 / Mean I/σ(I) obs: 8.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1BE9 minus peptide

1be9


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2398 1207 Random
Rwork0.2198 --
all0.2198 25906 -
obs0.2198 25691 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 0 172 1685
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.306
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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