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- PDB-8ufu: Structure of human endothelial nitric oxide synthase heme domain ... -

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Basic information

Entry
Database: PDB / ID: 8ufu
TitleStructure of human endothelial nitric oxide synthase heme domain in complex with 7-(9-amino-6,7,8,9-tetrahydro-5H-benzo[7]annulen-2-yl)-4-methylquinolin-2-amine
ComponentsNitric oxide synthase, endothelial
KeywordsOXIDOREDUCTASE / nitric oxide synthase inhibitor / heme enzyme
Function / homology
Function and homology information


regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / tetrahydrobiopterin metabolic process / NOSTRIN mediated eNOS trafficking / smooth muscle hyperplasia / regulation of nervous system process / superoxide-generating NAD(P)H oxidase activity / ovulation from ovarian follicle / pulmonary valve morphogenesis ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / tetrahydrobiopterin metabolic process / NOSTRIN mediated eNOS trafficking / smooth muscle hyperplasia / regulation of nervous system process / superoxide-generating NAD(P)H oxidase activity / ovulation from ovarian follicle / pulmonary valve morphogenesis / response to fluid shear stress / negative regulation of biomineral tissue development / Nitric oxide stimulates guanylate cyclase / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / aortic valve morphogenesis / arginine binding / endocardial cushion morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / cadmium ion binding / negative regulation of calcium ion transport / negative regulation of potassium ion transport / negative regulation of platelet activation / actin monomer binding / nitric oxide mediated signal transduction / blood vessel remodeling / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / nitric-oxide synthase activity / endothelial cell migration / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of blood pressure / regulation of sodium ion transport / response to hormone / nitric oxide metabolic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / homeostasis of number of cells within a tissue / removal of superoxide radicals / lung development / cell redox homeostasis / lipopolysaccharide-mediated signaling pathway / blood vessel diameter maintenance / VEGFR2 mediated vascular permeability / mitochondrion organization / negative regulation of smooth muscle cell proliferation / establishment of localization in cell / caveola / potassium ion transport / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / endocytic vesicle membrane / calcium ion transport / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to heat / scaffold protein binding / angiogenesis / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / response to lipopolysaccharide / in utero embryonic development / calmodulin binding / cytoskeleton / Extra-nuclear estrogen signaling / Golgi membrane / negative regulation of cell population proliferation / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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
Similarity search - Domain/homology
GADOLINIUM ATOM / PROTOPORPHYRIN IX CONTAINING FE / : / Nitric oxide synthase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 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, endothelial
B: Nitric oxide synthase, endothelial
C: Nitric oxide synthase, endothelial
D: Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,26841
Polymers197,3834
Non-polymers7,88437
Water6,521362
1
A: Nitric oxide synthase, endothelial
B: Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,58820
Polymers98,6922
Non-polymers3,89618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-196 kcal/mol
Surface area34040 Å2
MethodPISA
2
C: Nitric oxide synthase, endothelial
D: Nitric oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,68021
Polymers98,6922
Non-polymers3,98819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-197 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.673, 152.827, 109.162
Angle α, β, γ (deg.)90.00, 90.82, 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, endothelial / Constitutive NOS / cNOS / EC-NOS / Endothelial NOS / eNOS / NOS type III / NOSIII


Mass: 49345.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: endothelial / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29474, nitric-oxide synthase (NADPH)

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Non-polymers , 9 types, 399 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-WRI / (7M)-7-[(9S)-9-amino-6,7,8,9-tetrahydro-5H-benzo[7]annulen-2-yl]-4-methylquinolin-2-amine


Mass: 317.427 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H23N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#9: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.69 Å3/Da / Density % sol: 54.3 % / Description: rods
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10-12% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE, 0.1M GDCL3 10% GLYCEROL, 5 MM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2020 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→39.2 Å / Num. obs: 118090 / % possible obs: 96.5 % / Redundancy: 4.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.084 / Rrim(I) all: 0.18 / Χ2: 1 / Net I/σ(I): 5.4 / Num. measured all: 519769
Reflection shellResolution: 2.05→2.08 Å / Redundancy: 4.2 % / Rmerge(I) obs: 4.131 / Num. unique obs: 5346 / CC1/2: 0.282 / Rpim(I) all: 2.242 / Rrim(I) all: 4.716 / Χ2: 0.98 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→38.743 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.79 / Phase error: 34.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.256 11561 5.06 %random
Rwork0.2048 ---
obs0.2073 115990 94.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→38.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12815 0 508 362 13685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413825
X-RAY DIFFRACTIONf_angle_d1.02118830
X-RAY DIFFRACTIONf_dihedral_angle_d15.488032
X-RAY DIFFRACTIONf_chiral_restr0.0551938
X-RAY DIFFRACTIONf_plane_restr0.0062417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07160.51782970.49844707X-RAY DIFFRACTION63
2.0716-2.0960.44314070.44886834X-RAY DIFFRACTION89
2.096-2.12160.44913530.43696971X-RAY DIFFRACTION90
2.1216-2.14840.45153950.42137109X-RAY DIFFRACTION93
2.1484-2.17670.42823910.40197174X-RAY DIFFRACTION94
2.1767-2.20650.40593600.39727322X-RAY DIFFRACTION94
2.2065-2.2380.39834130.36967244X-RAY DIFFRACTION96
2.238-2.27140.36483660.34487358X-RAY DIFFRACTION96
2.2714-2.30690.37453590.3347441X-RAY DIFFRACTION96
2.3069-2.34470.36124500.31817240X-RAY DIFFRACTION96
2.3447-2.38520.32973400.30317429X-RAY DIFFRACTION96
2.3852-2.42850.3294090.2947351X-RAY DIFFRACTION96
2.4285-2.47520.36484040.30047084X-RAY DIFFRACTION92
2.4752-2.52570.33823700.27766817X-RAY DIFFRACTION90
2.5257-2.58070.29573780.24057559X-RAY DIFFRACTION97
2.5807-2.64070.31094200.247465X-RAY DIFFRACTION98
2.6407-2.70670.27764580.22797427X-RAY DIFFRACTION97
2.7067-2.77990.27823950.22247499X-RAY DIFFRACTION98
2.7799-2.86160.25593830.22157506X-RAY DIFFRACTION97
2.8616-2.9540.27024080.21017432X-RAY DIFFRACTION98
2.954-3.05950.3253400.21327516X-RAY DIFFRACTION97
3.0595-3.18190.29623590.21257426X-RAY DIFFRACTION96
3.1819-3.32670.29073690.20656934X-RAY DIFFRACTION90
3.3267-3.5020.24984390.17997534X-RAY DIFFRACTION98
3.502-3.72120.20944020.16487595X-RAY DIFFRACTION99
3.7212-4.00830.19053920.15287526X-RAY DIFFRACTION98
4.0083-4.41110.18313960.13587424X-RAY DIFFRACTION97
4.4111-5.04820.18363680.1297058X-RAY DIFFRACTION92
5.0482-6.35570.21123960.14917584X-RAY DIFFRACTION99
6.3557-38.7430.18863440.16837296X-RAY DIFFRACTION94
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)
10.9545-0.2348-0.29862.7995-0.41832.25630.21990.31830.33450.05570.14710.4238-0.7739-0.6475-0.28320.5840.15910.15320.5760.21440.488164.5631.843-186.062
21.0011-0.526-0.371.9679-0.35823.21730.0434-0.03410.04270.34570.08080.0408-0.1519-0.0692-0.12520.273-0.1274-0.0130.26830.02670.314374.88.446-158.221
30.69420.34790.17492.9380.07561.68050.1214-0.1533-0.19930.1738-0.06220.21740.5654-0.1057-0.04750.57540.0026-0.07630.33380.05980.365893.279-34.041-195.919
40.96320.510.46351.2627-0.02043.6032-0.03670.0697-0.0538-0.16610.1003-0.057-0.02820.184-0.06740.29750.062-0.01750.2023-0.00840.2846103.878-10.35-223.452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 68:480 )A68 - 480
2X-RAY DIFFRACTION2( CHAIN B AND RESID 68:480 )B68 - 480
3X-RAY DIFFRACTION3( CHAIN C AND RESID 68:480 )C68 - 480
4X-RAY DIFFRACTION4( CHAIN D AND RESID 68:480 )D68 - 480

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