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- PDB-1dww: MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER N-hydroxya... -

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Basic information

Entry
Database: PDB / ID: 1dww
TitleMURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DIMER N-hydroxyarginine and dihydrobiopterin
ComponentsNITRIC OXIDE SYNTHASE
KeywordsOXIDOREDUCTASE/TRANSFERASE / COMPLEX (OXIDOREDUCTASE-TRANSFERASE) / NITRIC OXIDE MONOOXYGENASE / HEME / DIMER / INTERMEDIATE / PTERIN / H2B / DIHYDROBIOPTERIN / OXIDOREDUCTASE-TRANSFERASE complex
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 / nitric-oxide synthase (NADPH) / blood vessel remodeling / 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-H2B / N-OMEGA-HYDROXY-L-ARGININE / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase, inducible
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.35 Å
AuthorsCrane, B.R. / Arvai, A.S. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
Citation
Journal: Biochemistry / Year: 2000
Title: Structures of the N(Omega)-Hydroxy-L-Arginine Complex of Inducible Nitric Oxide Synthase Oxygenase Dimer with Active Andinactive Pterins
Authors: Crane, B.R. / Arvai, A.S. / Ghosh, S. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
#1: Journal: Embo J. / Year: 1999
Title: N-Terminal Domain Swapping and Metal Ion Binding in Nitric Oxide Synthase Dimerization
Authors: Crane, B.R. / Rosenfeld, R.A. / Arvai, A.S. / Ghosh, D.K. / Ghosh, S. / Tainer, J.A. / Stuehr, D.J. / Getzoff, E.D.
#2: Journal: Embo J. / Year: 1999
Title: Inducible Nitric Oxide Synthase: Role of the N-Terminal Beta-Hairpin Hook and Pterin-Binding Segment in Dimerization and Tetrahydrobiopterin Interaction
Authors: Ghosh, D.K. / Crane, B.R. / Ghosh, S. / Wolan, D. / Gachhui, R. / Crooks, C. / Presta, A. / Tainer, J.A. / Getzoff, E.D. / Stuehr, D.J.
#3: 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.
#4: 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.
History
DepositionDec 14, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: KABSCH AND SANDER

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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)100,24418
Polymers97,2532
Non-polymers2,99116
Water12,448691
1
A: NITRIC OXIDE SYNTHASE
hetero molecules

A: NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,24418
Polymers97,2532
Non-polymers2,99116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area10680 Å2
ΔGint-221.07 kcal/mol
Surface area33920 Å2
MethodPISA
2
B: NITRIC OXIDE SYNTHASE
hetero molecules

B: NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,24418
Polymers97,2532
Non-polymers2,99116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+5/31
Buried area10510 Å2
ΔGint-225.67 kcal/mol
Surface area34100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.980, 212.980, 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-903-

ZN

21B-903-

ZN

31A-2274-

HOH

41A-2304-

HOH

51B-2138-

HOH

61B-2157-

HOH

71B-2219-

HOH

81B-2275-

HOH

91B-2306-

HOH

101B-2307-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.86387, -0.5037, -0.003907), (-0.503715, 0.863838, 0.007455), (0.00038, 0.008408, -0.999965)291.42731, 78.0866, 122.6879
2given(-0.866206, -0.499593, -0.009731), (-0.499653, 0.86621, 0.0051), (0.005881, 0.00928, -0.99994)291.86951, 77.4197, 122.7517
3given(-0.862943, -0.505143, -0.012623), (-0.505258, 0.862926, 0.008542), (0.006578, 0.013749, -0.999884)292.31, 78.3174, 121.1629
DetailsBIOLOGICAL_UNIT: INOS OXYGENASE DOMAIN ACTIVE AS A DIMER

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRIC OXIDE SYNTHASE / / INDUCIBLE NOS TYPE II / MAC-NOS


Mass: 48626.297 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 , 6 types, 707 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-H2B / 2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE / QUINONOID 7,8-TETRAHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N5O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-HAR / N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 190.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N4O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsEACH NOS DIMER IS COVALENTLY LINKED BY A TETRATHIOLATE ZINC CENTER THAT RESIDES ON THE MOLECULAR ...EACH NOS DIMER IS COVALENTLY LINKED BY A TETRATHIOLATE ZINC CENTER THAT RESIDES ON THE MOLECULAR SYMMETRY AXIS. DIHYDROBIOPTERIN IS BOUND IN A PROTONATED QUINONOID FORM AND POSITIVELY CHARGED NOH-L-ARGININE (HAR) IS LIKELY PROTONATED ON N OMEGA AT THE PH 6.0 OF THESE CRYSTALS
Sequence detailsPROTEIN WAS EXPRESSED WITH A COOH-TERMINAL HIS6 TAG.

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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 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
117 mg/mlprotein1drop
240 mMHEPPS1drop
310 %glycerol1drop
41 mMdithiothreitol1drop
54 mMNHA1drop
62 mM1dropH4B
72 mM4-amino-H4B1drop
850 mMMES1reservoir
950 mMbeta-octylglucoside1reservoir
1018-21 %1reservoirLi2SO4or ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 62465 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 46.9 Å2 / Rsym value: 0.074 / Net I/σ(I): 28.9
Reflection shellResolution: 2.35→2.43 Å / Mean I/σ(I) obs: 7.4 / Rsym value: 0.289 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 303449 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.289

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4phasing
X-PLORphasing
X-PLORrefinement
RefinementMethod to determine structure: OTHER / Resolution: 2.35→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3681934.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 3153 5.1 %RANDOM
Rwork0.249 ---
obs0.249 62465 98.7 %-
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1--12.53 Å2-9.2 Å20 Å2
2---12.53 Å20 Å2
3---25.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6848 0 188 691 7727
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.351.5
X-RAY DIFFRACTIONx_mcangle_it2.32
X-RAY DIFFRACTIONx_scbond_it1.932
X-RAY DIFFRACTIONx_scangle_it2.742.5
Refine LS restraints NCSRms dev Biso : 2.1 Å2 / Rms dev position: 0.04 Å / Weight Biso : 0.95 / Weight position: 100
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 472 4.9 %
Rwork0.362 9128 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.H
X-RAY DIFFRACTION3WATER_REP.PARAMTOPH19X.H
Software
*PLUS
Name: 'X-PLOR CNS 0.4' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25
LS refinement shell
*PLUS
Lowest resolution: 2.43 Å / Rfactor Rfree: 0.414 / Rfactor obs: 0.375

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