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- PDB-3fc5: G586S mutant nNOSoxy -

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Basic information

Entry
Database: PDB / ID: 3fc5
TitleG586S mutant nNOSoxy
ComponentsNitric oxide synthase, brain
KeywordsOXIDOREDUCTASE / nNOS / oxygenase / G586S / arginine / Alternative splicing / Calmodulin-binding / Cell membrane / Cell projection / FAD / FMN / Heme / Iron / Membrane / Metal-binding / 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 / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport / response to nitric oxide / nitric oxide metabolic process / postsynaptic specialization, intracellular component / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Ion homeostasis / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / calyx of Held / negative regulation of potassium ion transport / behavioral response to cocaine / negative regulation of calcium ion transport / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase (NADPH) / response to vitamin E / sodium channel regulator activity / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / negative regulation of insulin secretion / nitric oxide mediated signal transduction / multicellular organismal response to stress / nitric-oxide synthase activity / xenobiotic catabolic process / NADPH binding / arginine catabolic process / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / T-tubule / : / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to nutrient levels / response to hormone / secretory granule / response to activity / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / muscle contraction / cell periphery / establishment of localization in cell / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / potassium ion transport / establishment of protein localization / response to organic cyclic compound / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / cellular response to mechanical stimulus / response to estrogen / vasodilation / calcium ion transport / calcium-dependent protein binding / FMN binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / flavin adenine dinucleotide binding / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / negative regulation of neuron apoptotic process / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / calmodulin binding / response to hypoxia / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / synapse / dendrite / heme binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding
Similarity search - Function
Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily ...Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain 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 / 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 / PDZ domain / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ARGININE / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBruckmann, C. / Mowat, C.G.
CitationJournal: To be Published
Title: Oxygen Activation in Neuronal NO Synthase: Stabilisation of a Novel Intermediate in the G586S Mutant
Authors: Papale, D. / Bruckmann, C. / Miles, C.S. / Mowat, C.G. / Daff, S.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)99,8169
Polymers97,6852
Non-polymers2,1317
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-119 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.623, 110.276, 164.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPROPROchain A and (resseq 299:338 or resseq 350:716 )AA299 - 3383 - 42
12THRTHRTRPTRPchain A and (resseq 299:338 or resseq 350:716 )AA350 - 71654 - 420
21ARGARGPROPROchain B and (resseq 299:338 or resseq 350:716 )BB299 - 3383 - 42
22THRTHRTRPTRPchain B and (resseq 299:338 or resseq 350:716 )BB350 - 71654 - 420

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 48842.555 Da / Num. of mol.: 2 / Fragment: oxygenase domain, residues 297-718 / Mutation: G586S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NOS1 or BNOS / Plasmid: pCRNNR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P29476, nitric-oxide synthase (NADPH)

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Non-polymers , 5 types, 203 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#5: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 100mM Na-MES buffer (pH 5.8-6.0), 200mM ammonium acetate, 25mM L-arginine, 35microM sodium dodecyl sulfate(SDS), 5mM glutathione, 2% isopropanol, 22-24% (w/v) PEG 3350 , VAPOR DIFFUSION, temperature 291K
PH range: 5.8-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9737 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 2.59→35 Å / Num. all: 27819 / Num. obs: 27819 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.59→2.69 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.79 / Num. unique all: 2056 / % possible all: 70.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OM4

1om4


Resolution: 2.59→34.266 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.775 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 2000 7.2 %random
Rwork0.1987 25789 --
obs0.2027 27789 92.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.054 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 106.02 Å2 / Biso mean: 37.49 Å2 / Biso min: 19.71 Å2
Baniso -1Baniso -2Baniso -3
1-29.774 Å2-0 Å2-0 Å2
2---4.143 Å2-0 Å2
3----25.631 Å2
Refinement stepCycle: LAST / Resolution: 2.59→34.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 145 196 7003
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONf_bond_d70060.006
X-RAY DIFFRACTIONf_angle_d95321.047
X-RAY DIFFRACTIONf_chiral_restr9860.066
X-RAY DIFFRACTIONf_plane_restr12060.005
X-RAY DIFFRACTIONf_dihedral_angle_d252916.347
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3315X-RAY DIFFRACTIONPOSITIONAL0.051
12B3315X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5896-2.65430.3226980.24721269X-RAY DIFFRACTION66
2.6543-2.72610.33391130.24111455X-RAY DIFFRACTION74
2.7261-2.80630.3511270.24491642X-RAY DIFFRACTION85
2.8063-2.89680.28411380.22741780X-RAY DIFFRACTION90
2.8968-3.00030.32661480.23491900X-RAY DIFFRACTION98
3.0003-3.12030.32881490.22931933X-RAY DIFFRACTION98
3.1203-3.26220.27441540.21081961X-RAY DIFFRACTION99
3.2622-3.43410.2721530.20211980X-RAY DIFFRACTION99
3.4341-3.6490.23161510.18391954X-RAY DIFFRACTION99
3.649-3.93040.21431530.1681972X-RAY DIFFRACTION98
3.9304-4.32520.2361520.171966X-RAY DIFFRACTION98
4.3252-4.94950.20871520.15121954X-RAY DIFFRACTION98
4.9495-6.22970.20321540.17781984X-RAY DIFFRACTION96
6.2297-34.26880.23181580.19232039X-RAY DIFFRACTION94

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