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- PDB-2nsi: HUMAN INDUCIBLE NITRIC OXIDE SYNTHASE, ZN-FREE, SEITU COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2nsi
TitleHUMAN INDUCIBLE NITRIC OXIDE SYNTHASE, ZN-FREE, SEITU COMPLEX
ComponentsPROTEIN (NITRIC OXIDE SYNTHASE)
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / HEME PROTEIN / TETRAHYDROBIOPTERIN
Function / homology
Function and homology information


positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / peptidyl-cysteine S-nitrosylation / regulation of cellular respiration / Nitric oxide stimulates guanylate cyclase / prostaglandin secretion / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / superoxide metabolic process ...positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / peptidyl-cysteine S-nitrosylation / regulation of cellular respiration / Nitric oxide stimulates guanylate cyclase / prostaglandin secretion / ROS and RNS production in phagocytes / 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 / peroxisomal matrix / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of blood pressure / response to hormone / nitric oxide biosynthetic process / regulation of insulin secretion / cell redox homeostasis / innate immune response in mucosa / positive regulation of interleukin-8 production / response to bacterium / Peroxisomal protein import / 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 / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / defense response to Gram-negative bacterium / 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 / nucleoplasm / metal ion binding / nucleus / plasma membrane / 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
5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / ETHYLISOTHIOUREA / Nitric oxide synthase, inducible
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsLi, H. / Raman, C.S. / Glaser, C.B. / Blasko, E. / Young, T.A. / Parkinson, J.F. / Whitlow, M. / Poulos, T.L.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal structures of zinc-free and -bound heme domain of human inducible nitric-oxide synthase. Implications for dimer stability and comparison with endothelial nitric-oxide synthase.
Authors: Li, H. / Raman, C.S. / Glaser, C.B. / Blasko, E. / Young, T.A. / Parkinson, J.F. / Whitlow, M. / Poulos, T.L.
#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.
#2: Journal: Science / Year: 1997
Title: The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complex
Authors: Crane, B.R. / Arvai, A.S. / Gachhui, R. / Wu, C. / Ghosh, D.K. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal Structure of Constitutive Endothelial Nitric Oxide Synthase: A Paradigm for Pterin Function Involving a Novel Metal Center
Authors: Raman, C.S. / Li, H. / Martasek, P. / Kral, V. / Masters, B.S. / Poulos, T.L.
History
DepositionJan 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (NITRIC OXIDE SYNTHASE)
B: PROTEIN (NITRIC OXIDE SYNTHASE)
C: PROTEIN (NITRIC OXIDE SYNTHASE)
D: PROTEIN (NITRIC OXIDE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,53425
Polymers198,8224
Non-polymers4,71221
Water00
1
A: PROTEIN (NITRIC OXIDE SYNTHASE)
B: PROTEIN (NITRIC OXIDE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,81513
Polymers99,4112
Non-polymers2,40411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-115 kcal/mol
Surface area32730 Å2
MethodPISA
2
C: PROTEIN (NITRIC OXIDE SYNTHASE)
D: PROTEIN (NITRIC OXIDE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,71912
Polymers99,4112
Non-polymers2,30810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-120 kcal/mol
Surface area32760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.370, 188.370, 230.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.489109, -0.866926, 0.095976), (-0.869369, 0.475655, -0.133977), (0.070496, -0.148968, -0.986326)75.5454, 51.6729, 74.3981
2given(-0.855992, 0.516839, -0.012429), (-0.516982, -0.855621, 0.025329), (0.002457, 0.028107, 0.999602)45.431, 80.0917, 40.2717
3given(-0.016854, 0.990534, -0.136231), (0.998232, 0.024436, 0.054174), (0.05699, -0.135077, -0.989195)6.1553, -0.7844, 115.966

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Components

#1: Protein
PROTEIN (NITRIC OXIDE SYNTHASE) / E.C.1.14.13.39 OXIDOREDUCTASE / INOS


Mass: 49705.531 Da / Num. of mol.: 4 / Fragment: HEME DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: ADENOCARCINOMA DLD-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35228, nitric-oxide synthase (NADPH)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


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


Mass: 104.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8N2S
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: 5.13 Å3/Da / Density % sol: 78 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Temperature: 7 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22.0 mMGSH1drop
310 mML-Arg1drop
435 %satammonium sulfate1reservoir
530 %(v/v)glycerol1reservoir
650 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: MIRROR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 82161 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 66.8 Å2 / Rsym value: 0.092 / Net I/σ(I): 8.8
Reflection shellResolution: 3→3.05 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.699 / % possible all: 98.4
Reflection
*PLUS
Num. measured all: 355712 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.699

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.8refinement
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 3→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3614 5 %RANDOM
Rwork0.214 ---
obs0.214 70704 80.8 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13676 0 309 0 13985
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.183
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESIDUES 83-502 OF EACH SUBUNIT
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 346 5 %
Rwork0.299 5920 -
obs--57.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24

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