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- PDB-3ebd: Structure of inhibited murine iNOS oxygenase domain -

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Basic information

Entry
Database: PDB / ID: 3ebd
TitleStructure of inhibited murine iNOS oxygenase domain
ComponentsNitric oxide synthase, inducible
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / NOS / HEME / TETRAHYDROBIOPTERIN / OXIDOREDUCTASE Calmodulin-binding / FAD / FMN / Iron / Metal-binding / NADP / Polymorphism / Zinc
Function / homology
Function and homology information


Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton ...Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton / superoxide metabolic process / cGMP-mediated signaling / nitric-oxide synthase binding / cellular response to cytokine stimulus / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / regulation of insulin secretion / cellular response to organic cyclic compound / blood vessel remodeling / nitric-oxide synthase (NADPH) / response to tumor necrosis factor / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / positive regulation of interleukin-8 production / response to bacterium / Hsp90 protein binding / negative regulation of protein catabolic process / beta-catenin binding / regulation of blood pressure / peroxisome / positive regulation of interleukin-6 production / cellular response to type II interferon / circadian rhythm / cellular response to xenobiotic stimulus / FMN binding / flavin adenine dinucleotide binding / NADP binding / actin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / response to hypoxia / calmodulin binding / intracellular signal transduction / defense response to bacterium / cadherin binding / inflammatory response / positive regulation of apoptotic process / negative regulation of gene expression / heme binding / protein kinase binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-329 / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase, inducible
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGarcin, E.D. / Arvai, A.S. / Rosenfeld, R.J. / Kroeger, M.D. / Crane, B.R. / Andersson, G. / Andrews, G. / Hamley, P.J. / Mallinder, P.R. / Nicholls, D.J. ...Garcin, E.D. / Arvai, A.S. / Rosenfeld, R.J. / Kroeger, M.D. / Crane, B.R. / Andersson, G. / Andrews, G. / Hamley, P.J. / Mallinder, P.R. / Nicholls, D.J. / St-Gallay, S.A. / Tinker, A.C. / Gensmantel, N.P. / Mete, A. / Cheshire, D.R. / Connolly, S. / Stuehr, D.J. / Aberg, A. / Wallace, A.V. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase.
Authors: Garcin, E.D. / Arvai, A.S. / Rosenfeld, R.J. / Kroeger, M.D. / Crane, B.R. / Andersson, G. / Andrews, G. / Hamley, P.J. / Mallinder, P.R. / Nicholls, D.J. / St-Gallay, S.A. / Tinker, A.C. / ...Authors: Garcin, E.D. / Arvai, A.S. / Rosenfeld, R.J. / Kroeger, M.D. / Crane, B.R. / Andersson, G. / Andrews, G. / Hamley, P.J. / Mallinder, P.R. / Nicholls, D.J. / St-Gallay, S.A. / Tinker, A.C. / Gensmantel, N.P. / Mete, A. / Cheshire, D.R. / Connolly, S. / Stuehr, D.J. / Aberg, A. / Wallace, A.V. / Tainer, J.A. / Getzoff, E.D.
History
DepositionAug 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitric oxide synthase, inducible
B: Nitric oxide synthase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,70612
Polymers100,2422
Non-polymers2,46410
Water14,340796
1
A: Nitric oxide synthase, inducible
hetero molecules

A: Nitric oxide synthase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,70612
Polymers100,2422
Non-polymers2,46410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area9650 Å2
ΔGint-113 kcal/mol
Surface area33530 Å2
MethodPISA
2
B: Nitric oxide synthase, inducible
hetero molecules

B: Nitric oxide synthase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,70612
Polymers100,2422
Non-polymers2,46410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+5/31
Buried area9470 Å2
ΔGint-111 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.440, 213.440, 116.109
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-4397-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nitric oxide synthase, inducible / / E.C.1.14.13.39 / NOS TYPE II / INDUCIBLE NOS / INOS / MACROPHAGE NOS / MAC-NOS


Mass: 50120.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nos2, Inosl / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29477, nitric-oxide synthase (NADPH)

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Non-polymers , 5 types, 806 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN / Tetrahydrobiopterin


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#4: Chemical ChemComp-329 / (2S)-2-methyl-2,3-dihydrothieno[2,3-f][1,4]oxazepin-5-amine


Mass: 182.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N2OS
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 3.81 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→44.65 Å / Num. obs: 54828 / Biso Wilson estimate: 42.9 Å2

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
CNSphasing
RefinementResolution: 2.4→44.65 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 3423878 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2801 5.1 %RANDOM
Rwork0.215 ---
obs-54828 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 99.828 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 116.46 Å2 / Biso mean: 46.391 Å2 / Biso min: 16.48 Å2
Baniso -1Baniso -2Baniso -3
1--6.56 Å20 Å20 Å2
2---6.56 Å20 Å2
3---13.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6846 0 164 796 7806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.932.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramINH.top
X-RAY DIFFRACTION4param19x.hemeion.top
X-RAY DIFFRACTION5INH.partoph19x.heme

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