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- PDB-8ufq: Structure of human neuronal nitric oxide synthase R354A/G357D/E59... -

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Basic information

Entry
Database: PDB / ID: 8ufq
TitleStructure of human neuronal nitric oxide synthase R354A/G357D/E597Q mutant heme domain obtained after soaking crystal with 4-methyl-7-(4-methyl-2,3,4,5-tetrahydrobenzo[f][1,4]oxazepin-7-yl)quinolin-2-amine dihydrochloride
ComponentsNitric oxide synthase 1
KeywordsOXIDOREDUCTASE / nitric oxide synthase inhibitor / heme enzyme
Function / homology
Function and homology information


negative regulation of calcium ion transport into cytosol / myoblast fusion / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport ...negative regulation of calcium ion transport into cytosol / myoblast fusion / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / negative regulation of calcium ion transport / negative regulation of serotonin uptake / sodium channel regulator activity / striated muscle contraction / nitric-oxide synthase (NADPH) / regulation of cardiac muscle contraction / multicellular organismal response to stress / xenobiotic catabolic process / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / regulation of sodium ion transport / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / photoreceptor inner segment / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / cell redox homeostasis / sarcoplasmic reticulum / muscle contraction / cell periphery / sarcolemma / cellular response to growth factor stimulus / vasodilation / calcium-dependent protein binding / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / response to heat / scaffold protein binding / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia / cytoskeleton / calmodulin binding / membrane raft / synapse / heme binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Domain/homology
5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsLi, H. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
CitationJournal: Biochemistry / Year: 2024
Title: Crystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase.
Authors: Li, H. / Hardy, C.D. / Reidl, C.T. / Jing, Q. / Xue, F. / Cinelli, M. / Silverman, R.B. / Poulos, T.L.
History
DepositionOct 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase 1
B: Nitric oxide synthase 1
C: Nitric oxide synthase 1
D: Nitric oxide synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,46624
Polymers195,9834
Non-polymers4,48320
Water21,4921193
1
A: Nitric oxide synthase 1
B: Nitric oxide synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23312
Polymers97,9922
Non-polymers2,24110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-79 kcal/mol
Surface area33960 Å2
MethodPISA
2
C: Nitric oxide synthase 1
D: Nitric oxide synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23312
Polymers97,9922
Non-polymers2,24110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-80 kcal/mol
Surface area34140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.036, 51.554, 162.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Nitric oxide synthase 1 /


Mass: 48995.797 Da / Num. of mol.: 4 / Mutation: R354A, G357D, E597Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOS1 / Organ: brain / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29475

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Non-polymers , 5 types, 1213 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN / Tetrahydrobiopterin


Mass: 241.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N5O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1193 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.2 % / Description: plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 8% PEG3350 35mM citric acid 65mM Bis-Tris-Propane 10% glycerol 5mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2021 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→39.01 Å / Num. obs: 133216 / % possible obs: 100 % / Redundancy: 4.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.076 / Rrim(I) all: 0.166 / Net I/σ(I): 6.6 / Num. measured all: 612737
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 4.6 % / Rmerge(I) obs: 2.192 / Num. unique obs: 6450 / CC1/2: 0.407 / Rpim(I) all: 1.13 / Rrim(I) all: 2.474 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.98→38.683 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 12896 4.94 %random
Rwork0.1808 ---
obs0.1831 133189 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→38.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13631 0 302 1193 15126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714404
X-RAY DIFFRACTIONf_angle_d0.95319598
X-RAY DIFFRACTIONf_dihedral_angle_d17.9278445
X-RAY DIFFRACTIONf_chiral_restr0.052032
X-RAY DIFFRACTIONf_plane_restr0.0062481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00250.35154020.34288147X-RAY DIFFRACTION99
2.0025-2.02610.40763870.33648216X-RAY DIFFRACTION98
2.0261-2.05080.36274480.3338228X-RAY DIFFRACTION98
2.0508-2.07670.35954400.32038123X-RAY DIFFRACTION98
2.0767-2.1040.36784000.29918310X-RAY DIFFRACTION99
2.104-2.13290.32924070.28958357X-RAY DIFFRACTION98
2.1329-2.16330.30214040.27898277X-RAY DIFFRACTION99
2.1633-2.19560.33924330.26358200X-RAY DIFFRACTION99
2.1956-2.22990.36174410.29748258X-RAY DIFFRACTION99
2.2299-2.26650.30924290.25898269X-RAY DIFFRACTION99
2.2665-2.30560.28844330.23938255X-RAY DIFFRACTION99
2.3056-2.34750.28894420.22848374X-RAY DIFFRACTION99
2.3475-2.39260.27594250.22448191X-RAY DIFFRACTION99
2.3926-2.44150.29594210.22368331X-RAY DIFFRACTION99
2.4415-2.49450.27514210.20678183X-RAY DIFFRACTION98
2.4945-2.55260.26834160.20368341X-RAY DIFFRACTION99
2.5526-2.61640.27544740.19248158X-RAY DIFFRACTION99
2.6164-2.68710.29494430.20438343X-RAY DIFFRACTION100
2.6871-2.76610.25114300.19718255X-RAY DIFFRACTION99
2.7661-2.85540.23334550.18248351X-RAY DIFFRACTION99
2.8554-2.95740.24884100.17658256X-RAY DIFFRACTION99
2.9574-3.07580.2184500.17458297X-RAY DIFFRACTION99
3.0758-3.21570.2474940.17278205X-RAY DIFFRACTION99
3.2157-3.38520.20885000.15858216X-RAY DIFFRACTION99
3.3852-3.59710.19473580.14618312X-RAY DIFFRACTION99
3.5971-3.87460.1894370.1388377X-RAY DIFFRACTION99
3.8746-4.26410.16444550.12418316X-RAY DIFFRACTION99
4.2641-4.88010.16083860.12218271X-RAY DIFFRACTION99
4.8801-6.14440.16514290.14238313X-RAY DIFFRACTION100
6.1444-38.6830.16654260.15668327X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9333-0.12790.08070.52190.15561.6261-0.0322-0.038-0.0463-0.020.02340.05090.0117-0.02710.00310.2243-0.0030.03760.16610.04150.2119-34.0537.511-38.176
20.9203-0.2145-0.05540.55430.16962.2951-0.05340.01920.11810.02170.0171-0.0275-0.1070.11340.02760.2614-0.00610.00520.19230.0350.2124-34.0139.755-1.151
30.8920.25920.070.58430.16072.2872-0.0479-0.026-0.0995-0.02080.0107-0.03480.10410.1180.03140.24830.01050.00130.18990.03940.213424.45131.102-79.977
40.90280.1217-0.08670.51430.24821.6966-0.03250.02420.04770.02510.02160.0501-0.0427-0.01750.0080.22830.0051-0.03390.16920.05170.213724.65133.362-42.971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 303:722 )A303 - 722
2X-RAY DIFFRACTION2( CHAIN B AND RESID 304:722 )B304 - 722
3X-RAY DIFFRACTION3( CHAIN C AND RESID 303:722 )C303 - 722
4X-RAY DIFFRACTION4( CHAIN D AND RESID 304:722 )D304 - 722

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