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- PDB-1tll: CRYSTAL STRUCTURE OF RAT NEURONAL NITRIC-OXIDE SYNTHASE REDUCTASE... -

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Basic information

Entry
Database: PDB / ID: 1tll
TitleCRYSTAL STRUCTURE OF RAT NEURONAL NITRIC-OXIDE SYNTHASE REDUCTASE MODULE AT 2.3 A RESOLUTION.
ComponentsNitric-oxide synthase, brain
KeywordsOXIDOREDUCTASE / NITRIC-OXIDE SYNTHASE / REDUCTASE MODULE / FMN / FAD / NADP+
Function / homology
Function and homology information


Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / ROS and RNS production in phagocytes / postsynaptic specialization, intracellular component / azurophil granule / Ion homeostasis / synaptic signaling by nitric oxide ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / negative regulation of iron ion transmembrane transport / response to vitamin B3 / ROS and RNS production in phagocytes / postsynaptic specialization, intracellular component / 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 / positive regulation of sodium ion transmembrane transport / peptidyl-cysteine S-nitrosylase activity / negative regulation of cytosolic calcium ion concentration / positive regulation of the force of heart contraction / cadmium ion binding / neuron projection terminus / negative regulation of calcium ion transport / negative regulation of potassium ion transport / regulation of postsynaptic membrane potential / nitric-oxide synthase (NADPH) / sodium channel regulator activity / regulation of neurogenesis / : / nitric-oxide synthase activity / negative regulation of serotonin uptake / L-arginine catabolic process / xenobiotic catabolic process / multicellular organismal response to stress / NADPH binding / nitric oxide-cGMP-mediated signaling / postsynaptic density, intracellular component / regulation of sodium ion transport / nitric oxide metabolic process / striated muscle contraction / negative regulation of blood pressure / nitric oxide biosynthetic process / behavioral response to cocaine / photoreceptor inner segment / response to hormone / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / T-tubule / secretory granule / establishment of localization in cell / calyx of Held / positive regulation of long-term synaptic potentiation / response to activity / sarcoplasmic reticulum / cell periphery / response to nicotine / establishment of protein localization / female pregnancy / phosphoprotein binding / cellular response to mechanical stimulus / response to nutrient levels / negative regulation of insulin secretion / sarcolemma / caveola / response to estrogen / response to lead ion / response to peptide hormone / cellular response to growth factor stimulus / vasodilation / Z disc / calcium-dependent protein binding / NADP binding / FMN binding / flavin adenine dinucleotide binding / positive regulation of neuron apoptotic process / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / response to lipopolysaccharide / dendritic spine / cytoskeleton / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / response to ethanol / perikaryon / transmembrane transporter binding / response to hypoxia / calmodulin binding / mitochondrial outer membrane / 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
NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Flavodoxin domain / Translation factors / 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 ...NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Flavodoxin domain / Translation factors / 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 / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / SULFITE ION / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGarcin, E.D. / Bruns, C.M. / Lloyd, S.J. / Hosfield, D.J. / Tiso, M. / Gachhui, R. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase
Authors: Garcin, E.D. / Bruns, C.M. / Lloyd, S.J. / Hosfield, D.J. / Tiso, M. / Gachhui, R. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AFTER CHECKING THE ELECTRON DENSITY AND RESIDUES NEIGHBORING, THE AUTHORS CAME TO THE ...SEQUENCE AFTER CHECKING THE ELECTRON DENSITY AND RESIDUES NEIGHBORING, THE AUTHORS CAME TO THE CONCLUSION THAT THE PHE GIVEN IN THE SEQUENCE DATABASE IS REALLY A SER (RESIDUE 1008). THIS SERINE RESIDUE IS CONSERVED IN SEQUENCES OF NOS FOUND IN OTHER ORGANISMS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitric-oxide synthase, brain
B: Nitric-oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,14910
Polymers156,0192
Non-polymers4,1318
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.756, 69.174, 82.628
Angle α, β, γ (deg.)76.80, 72.07, 67.14
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nitric-oxide synthase, brain / NOS / type I / Neuronal NOS / N-NOS / nNOS / Constitutive NOS / NC-NOS / BNOS / reductase module


Mass: 78009.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NOS1, BNOS / Plasmid: pcW / Production host: Pichia pastoris (fungus) / References: UniProt: P29476, nitric-oxide synthase (NADPH)

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Non-polymers , 5 types, 231 molecules

#2: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.29 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4K, EDTA, Sodium-sulfite, Imidazole-Malate, DTT, glycerol, NADPH, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 65962 / Num. obs: 65962 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 6037 / Rsym value: 0.607 / % possible all: 91

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AM0

1am0


Resolution: 2.3→35.21 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1650028.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1909 3.5 %RANDOM
Rwork0.244 ---
all0.244 56259 --
obs0.244 55021 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1393 Å2 / ksol: 0.342472 e/Å3
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1--15.13 Å21.98 Å2-11.37 Å2
2--13.57 Å2-7.71 Å2
3---1.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9913 0 272 223 10408
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.43 250 3.7 %
Rwork0.423 6599 -
obs-6849 97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARA_TER.INPTOPO_TER.INP
X-RAY DIFFRACTION3NAPA.PARAMNAPA.TOPO
X-RAY DIFFRACTION4FMN.PARAMFMN.TOPO
X-RAY DIFFRACTION5FAD.PARAMFAD.TOPO

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