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- PDB-1nod: MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER (DELTA 65)... -

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Basic information

Entry
Database: PDB / ID: 1nod
TitleMURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER (DELTA 65) WITH TETRAHYDROBIOPTERIN AND SUBSTRATE L-ARGININE
ComponentsNITRIC OXIDE SYNTHASE
KeywordsCOMPLEX (OXIDOREDUCTASE/SUBSTRATE) / NITRIC OXIDE L-ARGININE MONOOXYGENASE / HEME / DIMER / NOS / COMPLEX (OXIDOREDUCTASE-SUBSTRATE) / COMPLEX (OXIDOREDUCTASE-SUBSTRATE) complex
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 / cellular response to cytokine stimulus / Fc-gamma receptor signaling pathway involved in phagocytosis / 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 / flavin adenine dinucleotide binding / NADP 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 / cytoplasm / cytosol
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
ARGININE / 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: 2.6 Å
AuthorsCrane, B.R. / Arvai, A.S. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
Citation
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.
#1: Journal: Science / Year: 1997
Title: The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complexes
Authors: Crane, B.R. / Arvai, A.S. / Gachhui, R. / Wu, C. / Ghosh, D.K. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
#2: Journal: Biochemistry / Year: 1997
Title: Characterization of the Inducible Nitric Oxide Synthase Oxygenase Domain Identifies a 49 Amino Acid Segment Required for Subunit Dimerization and Tetrahydrobiopterin Interaction
Authors: Ghosh, D.K. / Wu, C. / Pitters, E. / Moloney, M. / Werner, E.R. / Mayer, B. / Stuehr, D.J.
History
DepositionMar 5, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE
B: NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1599
Polymers97,9972
Non-polymers2,1627
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NITRIC OXIDE SYNTHASE
hetero molecules

A: NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,25510
Polymers97,9972
Non-polymers2,2588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area10930 Å2
ΔGint-123 kcal/mol
Surface area33840 Å2
MethodPISA
3
B: NITRIC OXIDE SYNTHASE
hetero molecules

B: NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0638
Polymers97,9972
Non-polymers2,0666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+5/31
Buried area10300 Å2
ΔGint-82 kcal/mol
Surface area33630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.000, 213.000, 114.200
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-1119-

HOH

21A-1122-

HOH

31A-1123-

HOH

41B-1180-

HOH

51B-1181-

HOH

61B-1182-

HOH

71B-1208-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.864913, -0.501901, -0.004529), (-0.50192, 0.864894, 0.005832), (0.00099, 0.007318, -0.999973)
Vector: 291.4567, 77.8202, 122.6254)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRIC OXIDE SYNTHASE


Mass: 48998.691 Da / Num. of mol.: 2 / Fragment: OXYGENASE DOMAIN 65-498
Source method: isolated from a genetically manipulated source
Details: MURINE INDUCIBLE / Source: (gene. exp.) Mus musculus (house mouse) / Cell: MACROPHAGE / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / References: UniProt: P29477, nitric-oxide synthase (NADPH)

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Non-polymers , 5 types, 325 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTWO ACTIVE CENTER STATES ARE PRESENT FOR EACH INDEPENDENT INOS SUBUNIT IN THE CRYSTAL LATTICE: 1) ...TWO ACTIVE CENTER STATES ARE PRESENT FOR EACH INDEPENDENT INOS SUBUNIT IN THE CRYSTAL LATTICE: 1) SUBSTRATE L-ARGININE (A906 OR B906) AND AN ASSOCIATED WATER (A1151 OR B1165) AT AN OCCUPANCY OF 0.55, AND 2) TWO ACTIVE CENTER MOLECULES (A1136 AND A1150 OR B1144 AND B1164) AT AN OCCUPANCY OF 0.45.
Has protein modificationY

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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: 4 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117 mg/mlprotein1drop
240 mMHepps1drop
310 %glycerol1drop
41 mMdithiothreitol1drop
58-10 mMH4B1drop
650 mMMES1reservoir
75 %(w/v)beta-octyl glucoside1reservoir
821 %1reservoiror ammonium sulfateLiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97
DetectorType: BRANDEIS / Detector: CCD / Date: Sep 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 45303 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 60.2 Å2 / Rsym value: 0.057 / Net I/σ(I): 22
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.344 / % possible all: 74.6
Reflection
*PLUS
Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 74.6 % / Rmerge(I) obs: 0.344

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NOC

1noc


Resolution: 2.6→20 Å / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: PRONOUNCED ANISOTROPIC DIFFRACTION COMPLICATED INDIVIDUAL B-FACTOR REFINEMENT. INDIVIDUAL B-FACTORS WERE REFINED TO MINIMIZE R-FREE AND PRODUCE AN AVERAGE VALUE COMMENSURATE WITH WILSON SCALING.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 -5 %RANDOM
Rwork0.229 ---
obs0.229 45303 95.3 %-
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å2-3.2 Å20 Å2
2---2 Å20 Å2
3----41.2 Å2
Refine analyzeLuzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 149 318 7208
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.831.5
X-RAY DIFFRACTIONx_mcangle_it4.522
X-RAY DIFFRACTIONx_scbond_it4.32
X-RAY DIFFRACTIONx_scangle_it6.592.5
Refine LS restraints NCSNCS model details: 71% OF BACKBONE / Rms dev Biso : 2 Å2 / Rms dev position: 100 Å / Weight Biso : 0 / Weight position: 0
LS refinement shellResolution: 2.6→2.7 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.445 222 5 %
Rwork0.395 3811 -
obs--74.6 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor obs: 0.395

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