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- PDB-1qau: UNEXPECTED MODES OF PDZ DOMAIN SCAFFOLDING REVEALED BY STRUCTURE ... -

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Entry
Database: PDB / ID: 1qau
TitleUNEXPECTED MODES OF PDZ DOMAIN SCAFFOLDING REVEALED BY STRUCTURE OF NNOS-SYNTROPHIN COMPLEX
ComponentsNEURONAL NITRIC OXIDE SYNTHASE (RESIDUES 1-130)
KeywordsOXIDOREDUCTASE / BETA-FINGER
Function / homology
Function and homology information


negative regulation of hepatic stellate cell contraction / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / postsynaptic specialization, intracellular component / ROS and RNS production in phagocytes / azurophil granule / Ion homeostasis / synaptic signaling by nitric oxide ...negative regulation of hepatic stellate cell contraction / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / postsynaptic specialization, intracellular component / ROS and RNS production in phagocytes / azurophil granule / Ion homeostasis / synaptic signaling by nitric oxide / negative regulation of vasoconstriction / response to nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / response to vitamin E / negative regulation of cytosolic calcium ion concentration / positive regulation of sodium ion transmembrane transport / peptidyl-cysteine S-nitrosylase activity / positive regulation of the force of heart contraction / cadmium ion binding / negative regulation of calcium ion transport / negative regulation of potassium ion transport / regulation of postsynaptic membrane potential / nitric oxide mediated signal transduction / sodium channel regulator activity / nitric-oxide synthase (NADPH) / regulation of neurogenesis / negative regulation of serotonin uptake / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / postsynaptic density, intracellular component / NADPH binding / L-arginine catabolic process / striated muscle contraction / nitric oxide-cGMP-mediated signaling / negative regulation of blood pressure / regulation of sodium ion transport / behavioral response to cocaine / response to hormone / nitric oxide metabolic process / photoreceptor inner segment / nitric oxide biosynthetic process / cellular response to epinephrine stimulus / T-tubule / sarcoplasmic reticulum membrane / secretory granule / calyx of Held / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / response to activity / cell periphery / response to nicotine / response to nutrient levels / phosphoprotein binding / establishment of protein localization / establishment of localization in cell / cellular response to mechanical stimulus / female pregnancy / negative regulation of insulin secretion / response to peptide hormone / sarcolemma / caveola / potassium ion transport / response to lead ion / cellular response to growth factor stimulus / response to estrogen / vasodilation / Z disc / calcium-dependent protein binding / calcium ion transport / FMN binding / NADP binding / flavin adenine dinucleotide binding / positive regulation of neuron apoptotic process / ATPase binding / response to heat / scaffold protein binding / response to ethanol / nuclear membrane / response to lipopolysaccharide / dendritic spine / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / mitochondrial outer membrane / calmodulin binding / response to hypoxia / cytoskeleton / postsynaptic density / membrane raft / negative regulation of cell population proliferation / heme binding / synapse / dendrite / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II
Similarity search - Function
PDZ domain / Pdz3 Domain / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain ...PDZ domain / Pdz3 Domain / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / PDZ domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsHillier, B.J. / Christopherson, K.S. / Prehoda, K.E. / Bredt, D.S. / Lim, W.A.
CitationJournal: Science / Year: 1999
Title: Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex.
Authors: Hillier, B.J. / Christopherson, K.S. / Prehoda, K.E. / Bredt, D.S. / Lim, W.A.
History
DepositionMar 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: NEURONAL NITRIC OXIDE SYNTHASE (RESIDUES 1-130)


Theoretical massNumber of molelcules
Total (without water)12,0331
Polymers12,0331
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.180, 38.990, 85.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NEURONAL NITRIC OXIDE SYNTHASE (RESIDUES 1-130)


Mass: 12032.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: P29476
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Vapor diffusion, sitting drop, pH 8.5, 298K, 15% PEG 4000, 100 mM Tris , VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotease1drop
2100 mMTris-HCl1reservoir
315 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 33078 / Num. obs: 33078 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 32.1
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.29 / Num. unique all: 3236 / % possible all: 99
Reflection
*PLUS
Num. measured all: 131703

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.25→50 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 3201 -RANDOM
Rwork0.2388 ---
all-31989 --
obs-31989 95.8 %-
Refinement stepCycle: LAST / Resolution: 1.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 0 73 885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d1.39
X-RAY DIFFRACTIONc_angle_deg1.39
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.255 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.7 Å2

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