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- PDB-8ufs: Structure of human endothelial nitric oxide synthase E361Q mutant... -

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Basic information

Entry
Database: PDB / ID: 8ufs
TitleStructure of human endothelial nitric oxide synthase E361Q mutant heme domain obtain 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 3
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 / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / positive regulation of guanylate cyclase activity / 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 potassium ion transport / negative regulation of platelet activation / negative regulation of calcium ion transport / actin monomer binding / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / blood vessel remodeling / nitric-oxide synthase activity / eNOS activation / nitric oxide mediated signal transduction / arginine catabolic process / homeostasis of number of cells within a tissue / regulation of sodium ion transport / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / nitric oxide biosynthetic process / negative regulation of blood pressure / blood vessel diameter maintenance / removal of superoxide radicals / mitochondrion organization / response to hormone / cell redox homeostasis / VEGFR2 mediated vascular permeability / caveola / negative regulation of smooth muscle cell proliferation / establishment of localization in cell / lung development / potassium ion transport / regulation of blood pressure / vasodilation / endocytic vesicle membrane / positive regulation of angiogenesis / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to heat / scaffold protein binding / angiogenesis / in utero embryonic development / response to lipopolysaccharide / Extra-nuclear estrogen signaling / cytoskeleton / calmodulin binding / negative regulation of cell population proliferation / Golgi membrane / heme binding / positive regulation of gene expression / Golgi apparatus / 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 / Flavoprotein-like superfamily
Similarity search - Domain/homology
GADOLINIUM ATOM / 5,6,7,8-TETRAHYDROBIOPTERIN / 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 3
B: Nitric oxide synthase 3
C: Nitric oxide synthase 3
D: Nitric oxide synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,76543
Polymers197,3794
Non-polymers7,38639
Water12,881715
1
A: Nitric oxide synthase 3
B: Nitric oxide synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,84623
Polymers98,6902
Non-polymers4,15721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-152 kcal/mol
Surface area33360 Å2
MethodPISA
2
C: Nitric oxide synthase 3
D: Nitric oxide synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,91920
Polymers98,6902
Non-polymers3,22918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-153 kcal/mol
Surface area33600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.821, 152.240, 108.492
Angle α, β, γ (deg.)90.00, 90.78, 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 3 /


Mass: 49344.785 Da / Num. of mol.: 4 / Mutation: E361Q
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

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Non-polymers , 9 types, 754 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-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
#4: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: 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
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Gd
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
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: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2021
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→39.1 Å / Num. obs: 118594 / % possible obs: 97.8 % / Redundancy: 3.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.096 / Rrim(I) all: 0.174 / Χ2: 0.78 / Net I/σ(I): 4.8 / Num. measured all: 368104
Reflection shellResolution: 2.05→2.09 Å / % possible obs: 94.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 1.194 / Num. measured all: 15981 / Num. unique obs: 5663 / CC1/2: 0.395 / Rpim(I) all: 0.879 / Rrim(I) all: 1.493 / Χ2: 0.49 / Net I/σ(I) obs: 1.3

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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: 2.05→39.1 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 10195 5.04 %random
Rwork0.1845 ---
obs0.187 115538 84.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12824 0 451 715 13990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913702
X-RAY DIFFRACTIONf_angle_d0.97918654
X-RAY DIFFRACTIONf_dihedral_angle_d14.6058003
X-RAY DIFFRACTIONf_chiral_restr0.0541942
X-RAY DIFFRACTIONf_plane_restr0.0062398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.07340.35112700.28634235X-RAY DIFFRACTION56
2.0734-2.09780.29573160.24915342X-RAY DIFFRACTION71
2.0978-2.12340.29283280.25515517X-RAY DIFFRACTION72
2.1234-2.15030.32583010.25165613X-RAY DIFFRACTION74
2.1503-2.17860.30433020.24686035X-RAY DIFFRACTION80
2.1786-2.20840.28553090.23186343X-RAY DIFFRACTION83
2.2084-2.240.28063480.23956363X-RAY DIFFRACTION84
2.24-2.27340.29413030.23746527X-RAY DIFFRACTION85
2.2734-2.30890.29813470.22726551X-RAY DIFFRACTION85
2.3089-2.34680.28953720.2226414X-RAY DIFFRACTION86
2.3468-2.38720.26133150.21816522X-RAY DIFFRACTION85
2.3872-2.43060.27723790.22166467X-RAY DIFFRACTION86
2.4306-2.47740.27313370.22636278X-RAY DIFFRACTION82
2.4774-2.52790.28673300.20756204X-RAY DIFFRACTION82
2.5279-2.58290.25493250.19356667X-RAY DIFFRACTION86
2.5829-2.64290.23473810.19246545X-RAY DIFFRACTION88
2.6429-2.7090.24763870.18946604X-RAY DIFFRACTION87
2.709-2.78220.24043460.1916636X-RAY DIFFRACTION88
2.7822-2.86410.22113360.19776671X-RAY DIFFRACTION87
2.8641-2.95650.23253640.19966669X-RAY DIFFRACTION88
2.9565-3.06210.26853040.18666774X-RAY DIFFRACTION89
3.0621-3.18470.25643180.19346688X-RAY DIFFRACTION87
3.1847-3.32960.24233730.18946415X-RAY DIFFRACTION84
3.3296-3.5050.24693780.18016808X-RAY DIFFRACTION90
3.505-3.72440.23243760.16366864X-RAY DIFFRACTION90
3.7244-4.01170.18183540.14936910X-RAY DIFFRACTION91
4.0117-4.4150.18223690.14066805X-RAY DIFFRACTION90
4.415-5.05270.19053310.13086681X-RAY DIFFRACTION87
5.0527-6.36140.19913680.15197013X-RAY DIFFRACTION92
6.3614-39.10.19433280.18896921X-RAY DIFFRACTION90
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)
10.48660.1235-0.14880.7976-0.25260.84090.25530.53190.2440.08250.18910.2347-0.5495-0.5560.09930.51070.23680.20720.4460.32020.361464.59431.76-184.961
20.9529-0.1795-0.32210.8496-0.39631.52610.1036-0.00530.04250.14760.04760.0028-0.0838-0.105-0.11050.1778-0.0364-0.01930.14640.01660.203674.5998.452-157.207
30.4648-0.06090.17711.3397-0.0830.94050.072-0.2186-0.17540.08990.06180.16990.3311-0.0998-0.04550.30870.0128-0.0510.23850.10330.290593.417-34.068-194.813
40.71260.21820.16780.5841-0.07151.3239-0.01750.0124-0.0357-0.04230.0573-0.01730.01020.0862-0.02880.12830.0379-0.02320.1304-0.00440.1771103.808-10.357-222.007
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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