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- PDB-1m8i: inducible nitric oxide synthase with 5-nitroindazole bound -

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Basic information

Entry
Database: PDB / ID: 1m8i
Titleinducible nitric oxide synthase with 5-nitroindazole bound
Componentsinducible Nitric oxide synthase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / peptidyl-cysteine S-nitrosylation / Peroxisomal protein import / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / superoxide metabolic process / regulation of cytokine production involved in inflammatory response / cortical cytoskeleton ...Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / peptidyl-cysteine S-nitrosylation / Peroxisomal protein import / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / superoxide metabolic process / regulation of cytokine production involved in inflammatory response / cortical cytoskeleton / Fc-gamma receptor signaling pathway involved in phagocytosis / cellular response to cytokine stimulus / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / nitric oxide biosynthetic process / regulation of insulin secretion / positive regulation of interleukin-8 production / response to bacterium / circadian rhythm / negative regulation of protein catabolic process / cellular response to type II interferon / positive regulation of interleukin-6 production / cellular response to xenobiotic stimulus / peroxisome / FMN binding / NADP binding / flavin adenine dinucleotide binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / calmodulin binding / response to hypoxia / defense response to bacterium / inflammatory response / negative regulation of gene expression / heme binding / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / 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, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 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, 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
5-NITROINDAZOLE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRosenfeld, R.J. / Garcin, E.D. / Panda, K. / Andersson, G. / Aberg, A. / Wallace, A.V. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D.
Citation
Journal: Biochemistry / Year: 2002
Title: Conformational Changes in Nitric Oxide Synthases Induced by Chlorzoxazone and Nitroindazoles: Crystallographic and Computational Analyses of Inhibitor Potency
Authors: Rosenfeld, R.J. / Garcin, E.D. / Panda, K. / Andersson, G. / Aberg, A. / Wallace, A.V. / Morris, G.M. / Olson, A.J. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D.
#1: Journal: Science / Year: 1998
Title: Structure of nitric oxide synthase oxygenase dimer with pterin and substrate
Authors: Crane, B.R. / Arvai, A.S. / Ghosh, D.K. / Wu, C. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
History
DepositionJul 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_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_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,4588
Polymers100,4162
Non-polymers2,0426
Water1,38777
1
A: inducible Nitric oxide synthase
hetero molecules

A: inducible Nitric oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4588
Polymers100,4162
Non-polymers2,0426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area8940 Å2
ΔGint-56 kcal/mol
Surface area34300 Å2
MethodPISA, PQS
2
B: inducible Nitric oxide synthase
hetero molecules

B: inducible Nitric oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4588
Polymers100,4162
Non-polymers2,0426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+5/31
Buried area8960 Å2
ΔGint-56 kcal/mol
Surface area33580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)213.962, 213.962, 114.524
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1042-

HOH

21A-1086-

HOH

31A-1092-

HOH

41B-1026-

HOH

51B-1091-

HOH

DetailsBiologically active as a dimer. To get one biological dimer, apply the following symmetry operation to chain A: 1+y-x, y, 1/2-z / To get a second biological dimer, apply the following symmetry operation to chain B: 2-x, 1-x+y, 2/3-z+5/3

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Components

#1: Protein inducible Nitric oxide synthase / NOS / type II / Inducible NOS / iNOS / Macrophage NOS / MAC-NOS


Mass: 50208.027 Da / Num. of mol.: 2 / Fragment: oxygenase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / References: UniProt: P29477, nitric-oxide synthase (NADPH)
#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-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Chemical ChemComp-5NI / 5-NITROINDAZOLE


Mass: 163.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.77 Å3/Da / Density % sol: 67.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Lithium Sulfate, B-octyl-glucodise, MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
240 mMEPPS1droppH7.6
31 mMdithiothreitol1drop
40.002 mMBH41drop
520-30 %1reservoirLi2SO4
65 %beta-octylglucoside1reservoir
750 mMMES1reservoirpH5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 36964 / Num. obs: 36964 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2312 / Rsym value: 0.326 / % possible all: 55
Reflection
*PLUS
Num. measured all: 85604 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 55 % / Num. unique obs: 2312 / Num. measured obs: 4659

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1DF1

1df1


Resolution: 2.7→19.93 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1865 5 %RANDOM
Rwork0.238 ---
all-36964 --
obs-36964 86.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.7884 Å2 / ksol: 0.276543 e/Å3
Displacement parametersBiso mean: 64.4 Å2
Baniso -1Baniso -2Baniso -3
1--22.53 Å2-4.39 Å20 Å2
2---22.53 Å20 Å2
3---45.05 Å2
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.55 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6716 0 144 77 6937
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.732.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 191 4.7 %
Rwork0.341 3861 -
obs-2312 58 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION45NITRO_FLEX.PAR5NITRO_FLEX.TOP
X-RAY DIFFRACTION5MISC.PARMISC.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22

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