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- PDB-1jwk: Murine Inducible Nitric Oxide Synthase Oxygenase Dimer (Delta 65)... -

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Basic information

Entry
Database: PDB / ID: 1jwk
TitleMurine Inducible Nitric Oxide Synthase Oxygenase Dimer (Delta 65) with W457A Mutation at Tetrahydrobiopterin Binding Site
ComponentsNitric Oxide Synthase, Inducible
KeywordsOXIDOREDUCTASE / Nitric Oxide L-Arginine Monooxygenase / Heme / Dimer / NOS / Tetrahydrobiopterin
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 / cortical cytoskeleton / regulation of cytokine production involved in inflammatory response ...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 / cortical cytoskeleton / regulation of cytokine production involved in inflammatory response / 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 / negative regulation of protein catabolic process / cellular response to type II interferon / positive regulation of interleukin-6 production / circadian rhythm / peroxisome / FMN binding / cellular response to xenobiotic stimulus / flavin adenine dinucleotide binding / NADP binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / response to hypoxia / calmodulin binding / 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
7,8-DIHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase, inducible
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAoyagi, M. / Arvai, A.S. / Ghosh, S. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D.
Citation
Journal: Biochemistry / Year: 2001
Title: Structures of tetrahydrobiopterin binding-site mutants of inducible nitric oxide synthase oxygenase dimer and implicated roles of Trp457.
Authors: Aoyagi, M. / Arvai, A.S. / Ghosh, S. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D.
#1: Journal: Biochemistry / Year: 2001
Title: A Conserved Tryptophan in Nitric Oxide Synthase Regulates Heme-dioxy Reduction by Tetrahydrobiopterin
Authors: Wang, Z.-Q. / Wei, C.-C. / Ghosh, S. / Meade, A.L. / Hemann, C. / Hille, R. / Stuehr, D.J.
History
DepositionSep 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)102,73011
Polymers100,2182
Non-polymers2,5129
Water8,305461
1
A: Nitric Oxide Synthase, Inducible
hetero molecules

A: Nitric Oxide Synthase, Inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,82212
Polymers100,2182
Non-polymers2,60410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area9460 Å2
ΔGint-59 kcal/mol
Surface area34580 Å2
MethodPISA, PQS
2
B: Nitric Oxide Synthase, Inducible
hetero molecules

B: Nitric Oxide Synthase, Inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,63810
Polymers100,2182
Non-polymers2,4208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+5/31
Buried area9270 Å2
ΔGint-52 kcal/mol
Surface area35920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)213.479, 213.479, 116.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer generated from each subunit, A and B, in the assymetric unit by the operation 1+y-x, y, 1/2-z and 2-x, 1-x+y, 2/3-z+5/3, respectively.

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Components

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Protein / Sugars , 2 types, 4 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: 50108.961 Da / Num. of mol.: 2 / Fragment: Oxygenase domain 66-498 / Mutation: YES
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: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 468 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N5O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 67.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
240 mMEPPS1drop
327-30 %satammonium sulfate1reservoir
450 mMMES1reservoir
510-30 mMBOG1reservoir
615-30 mMdithiothreitol1reservoir

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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: Nov 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 490274 / Num. obs: 63261 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.75 % / Biso Wilson estimate: 29.2 Å2 / Rsym value: 0.04 / Net I/σ(I): 31.6
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.8 / Num. unique all: 4071 / Rsym value: 0.38 / % possible all: 59.7
Reflection
*PLUS
Num. measured all: 490274 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 59.7 % / Rmerge(I) obs: 0.38

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NOD

1nod


Resolution: 2.3→19.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 922300.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4846 5.1 %RANDOM
Rwork0.218 ---
obs0.218 63261 91.4 %-
all-490274 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.75 Å2 / ksol: 0.32688 e/Å3
Displacement parametersBiso mean: 45.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.98 Å21.83 Å20 Å2
2---5.98 Å20 Å2
3---11.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6716 0 174 461 7351
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_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 317 5.2 %
Rwork0.292 5702 -
obs-7823 53 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
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_deg1.14
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.321 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.292

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