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- PDB-2qkv: Crystal Structure of the C645S Mutant of the 5th PDZ Domain of InaD -

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Basic information

Entry
Database: PDB / ID: 2qkv
TitleCrystal Structure of the C645S Mutant of the 5th PDZ Domain of InaD
ComponentsInactivation-no-after-potential D protein
KeywordsPEPTIDE BINDING PROTEIN / PDZ DOMAIN / SCAFFOLDING PROTEIN / Membrane / Sensory transduction / Vision
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 / 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 / SAD / Resolution: 1.55 Å
AuthorsRanganathan, R. / Socolich, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Dynamic Scaffolding in a G Protein-Coupled Signaling System.
Authors: Mishra, P. / Socolich, M. / Wall, M.A. / Graves, J. / Wang, Z. / Ranganathan, R.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inactivation-no-after-potential D protein
B: Inactivation-no-after-potential D protein


Theoretical massNumber of molelcules
Total (without water)20,6422
Polymers20,6422
Non-polymers00
Water2,576143
1
A: Inactivation-no-after-potential D protein

A: Inactivation-no-after-potential D protein

A: Inactivation-no-after-potential D protein

B: Inactivation-no-after-potential D protein

B: Inactivation-no-after-potential D protein

B: Inactivation-no-after-potential D protein


Theoretical massNumber of molelcules
Total (without water)61,9256
Polymers61,9256
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation13_554y+1/4,x+3/4,-z-1/41
crystal symmetry operation17_554x+1/4,z+3/4,-y-1/41
crystal symmetry operation21_554z+1/4,y+3/4,-x-1/41
Buried area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.040, 112.040, 112.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
DetailsThe biological assembly is unknown.

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Components

#1: Protein Inactivation-no-after-potential D protein


Mass: 10320.834 Da / Num. of mol.: 2 / Fragment: 5th PDZ domain / Mutation: C645S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD / Plasmid: pGEX-5X-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24008
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3M Na Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONAPS 19-BM20.9794
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMay 19, 2002Double crystal, Si(111)
SBC2CCDAug 23, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
ReflectionResolution: 1.55→40 Å / Num. obs: 36464 / % possible obs: 99.9 % / Rsym value: 0.052 / Net I/σ(I): 51.1
Reflection shellResolution: 1.55→2.08 Å / Mean I/σ(I) obs: 4.4 / Rsym value: 0.504 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNS0.3refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→30 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3324 5 %RANDOM
Rwork0.248 ---
obs0.248 33401 99.8 %-
Displacement parametersBiso mean: 24.888 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 0 143 1548
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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