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- PDB-3dwj: Heme-proximal W188H mutant of inducible nitric oxide synthase -

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Basic information

Entry
Database: PDB / ID: 3dwj
TitleHeme-proximal W188H mutant of inducible nitric oxide synthase
ComponentsNitric oxide synthase, inducible
KeywordsOXIDOREDUCTASE / NITRIC OXIDE MONOOXYGENASE / HEME / PTERIN / DIMER / NOS / Calmodulin-binding / FAD / FMN / Iron / Metal-binding / NADP / Polymorphism / Zinc
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 / positive regulation of killing of cells of another organism / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / cGMP-mediated signaling ...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 / positive regulation of killing of cells of another organism / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / cGMP-mediated signaling / superoxide metabolic process / cortical cytoskeleton / nitric-oxide synthase binding / peptidyl-cysteine S-nitrosylation / cellular response to cytokine stimulus / regulation of cytokine production involved in inflammatory response / cellular response to organic cyclic compound / blood vessel remodeling / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / response to tumor necrosis factor / nitric-oxide synthase activity / arginine catabolic process / nitric oxide biosynthetic process / negative regulation of blood pressure / regulation of insulin secretion / response to hormone / positive regulation of interleukin-8 production / response to bacterium / Hsp90 protein binding / negative regulation of protein catabolic process / cellular response to type II interferon / beta-catenin binding / regulation of blood pressure / positive regulation of interleukin-6 production / circadian rhythm / cellular response to xenobiotic stimulus / peroxisome / FMN binding / flavin adenine dinucleotide binding / NADP binding / regulation of cell population proliferation / actin binding / cellular response to lipopolysaccharide / response to lipopolysaccharide / response to hypoxia / calmodulin binding / intracellular signal transduction / defense response to bacterium / inflammatory response / cadherin binding / 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 / nucleus / metal ion binding / 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, 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 / AMMONIUM ION / Nitric oxide synthase, inducible
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTejero, J. / Biswas, A. / Wang, Z.-Q. / Haque, M.M. / Hemann, C. / Zweier, J.L. / Page, R.C. / Misra, S. / Stuehr, D.J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Stabilization and Characterization of a Heme-Oxy Reaction Intermediate in Inducible Nitric-oxide Synthase
Authors: Tejero, J. / Biswas, A. / Wang, Z.Q. / Page, R.C. / Haque, M.M. / Hemann, C. / Zweier, J.L. / Misra, S. / Stuehr, D.J.
History
DepositionJul 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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

Downloads & links

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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)101,5079
Polymers99,6592
Non-polymers1,8487
Water5,819323
1
A: Nitric oxide synthase, inducible
hetero molecules

A: Nitric oxide synthase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,60310
Polymers99,6592
Non-polymers1,9448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area10440 Å2
ΔGint-108.4 kcal/mol
Surface area33580 Å2
MethodPISA
2
B: Nitric oxide synthase, inducible
hetero molecules

B: Nitric oxide synthase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4118
Polymers99,6592
Non-polymers1,7526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Buried area10530 Å2
ΔGint-78.1 kcal/mol
Surface area33540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.597, 214.597, 111.933
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-1029-

HOH

21B-1127-

HOH

31B-1134-

HOH

41B-1140-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nitric oxide synthase, inducible / NOS type II / Inducible NO synthase / Inducible NOS / iNOS / Macrophage NOS / MAC- NOS


Mass: 49829.676 Da / Num. of mol.: 2 / Fragment: OXYGENASE DOMAIN 66-496 / Mutation: W188H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nos2, Inosl / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29477, nitric-oxide synthase (NADPH)

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Non-polymers , 5 types, 330 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#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 / Comment: neurotransmitter*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 277 K / pH: 5.3
Details: 0.7-1.2M (NH4)2SO4, 0.1M MES, pH 4.9-5.7, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→43.8 Å / Num. obs: 37844 / % possible obs: 95 % / Observed criterion σ(I): 5 / Redundancy: 4.53 % / Biso Wilson estimate: 55.47 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.7
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.49 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.1 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIXphenixrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NOD

1nod


Resolution: 2.75→43.77 Å / SU ML: 0.45 / Phase error: 34.57 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.294 3507 5.07 %
Rwork0.226 --
obs0.229 37844 92.3 %
all-37844 -
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.49 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 73.11 Å2
Baniso -1Baniso -2Baniso -3
1--10.75 Å20 Å20 Å2
2---10.75 Å2-0 Å2
3---21.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.75→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6677 0 127 323 7127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097011
X-RAY DIFFRACTIONf_angle_d1.4869565
X-RAY DIFFRACTIONf_dihedral_angle_d20.22505
X-RAY DIFFRACTIONf_chiral_restr0.1990
X-RAY DIFFRACTIONf_plane_restr0.0081220
LS refinement shellResolution: 2.75→2.79 Å
RfactorNum. reflection% reflection
Rfree0.467 165 -
Rwork0.367 2577 -
obs--92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4993-0.4099-7.14290.8369-3.5289-2.16080.3489-1.3876-0.00870.3142-0.41860.07130.45990.8459-0.56510.3660.023-0.26650.5621-0.250.011870.5713-40.987.4462
20.31240.4050.80254.37111.34470.54230.30010.07620.09210.8049-0.4072-0.92670.19370.00560.10380.43820.0963-0.26740.5582-0.27110.443577.7754-42.51251.3284
31.1250.19551.2110.3718-0.42871.00920.14510.0457-0.253-0.11460.0266-0.60640.11640.5417-0.26290.30610.07060.04780.4218-0.10060.820698.161-26.8678-11.1041
45.71470.54092.26990.30922.0069-0.6277-0.51610.60651.54540.3234-0.6068-0.61770.75720.31141.31150.36860.08360.20360.46330.11580.925997.7062-18.0322-26.1206
50.6567-1.0662-1.1160.4774-0.78610.96820.1024-0.12591.25310.0022-0.5167-0.7572-0.3542-0.17940.26330.29340.0433-0.03130.4171-0.08870.758798.4473-18.453-12.1659
6-0.1481-1.3909-0.35430.0113-0.9580.87930.0724-0.07580.86660.1229-0.3110.5382-0.2353-0.06880.220.34550.0796-0.04190.4038-0.24640.803481.7153-15.2397-7.7894
73.21851.33890.59020.8869-0.3480.62610.3051-0.1051.5155-0.0318-0.55840.04340.1639-0.02140.32320.48990.0236-0.01570.486-0.38420.930382.3075-12.3125-2.6501
80.1705-2.78591.30184.98860.55383.07350.1078-0.55891.29830.4176-0.373-0.54930.35030.459-0.29670.2676-0.010.00920.3064-0.48210.32671.9926-17.16527.131
99.335-0.8309-2.68230.8054-1.4611-2.07281.6103-1.09350.02340.3036-1.33470.1120.5633-0.9949-0.50750.4758-0.40680.08211.1052-0.55330.414563.1912-22.216915.3873
108.5122-1.8672-3.46490.02120.19780.69850.4539-1.24082.13291.028-0.32990.05980.1828-0.1223-0.12170.4997-0.14520.02590.8097-0.66540.52775.0996-13.557713.6128
112.67962.7172-0.18010.68770.57460.1775-0.1616-0.60271.2841-0.2043-0.25220.8699-0.3445-0.1960.3750.39310.07720.00710.508-0.50281.753654.5041-10.5120.5505
120.4999-0.58660.25261.99290.55-0.36-0.20730.0324-0.0765-0.0087-0.15030.41040.10880.05480.37550.50350.0768-0.06960.5067-0.25730.717376.1286-19.2635-4.483
13-2.0078-1.08-1.06045.13370.28461.01410.2872-0.02280.16060.7063-0.18151.0324-0.1045-0.0895-0.07170.2163-0.00480.09310.3929-0.49380.945450.8185-26.0313.3966
144.95530.6365-1.54822.2062-0.35531.6859-0.04990.2211.0639-0.1277-0.17550.846-0.1012-0.40560.22530.31350.0822-0.190.1813-0.31040.519360.06-22.3687-13.4614
152.56291.09232.98510.77370.6622-1.11450.0099-0.22360.7001-0.25-0.11710.3359-0.1229-0.16680.12790.30580.0514-0.08960.4605-0.22940.366672.6491-31.5534-10.4202
166.08875.35031.8675-7.7831-5.6087-3.83340.62331.6259-0.49220.1222-0.02740.4660.22990.6845-1.18750.57850.2162-0.19211.1631-0.17560.981886.6479-24.306615.0142
170.2957-1.1449-1.36351.0594-1.75370.3586-0.01610.7344-0.3283-0.6517-0.0242-0.1038-0.14920.13830.07110.46320.09020.14790.6118-0.22440.482285.69934.274141.4654
182.03923.49131.26317.2383-2.03639.73691.1926-0.50021.55370.095-2.15010.34281.3650.95960.73540.4640.0780.15890.7311-0.37930.783283.5299-3.591648.6746
191.03450.74821.5081-0.26870.07310.5483-0.05620.4457-0.1857-0.1788-0.632-0.79930.22820.38940.6250.3930.05560.03490.5377-0.10680.83196.5755-22.569754.0824
202.91651.9405-0.4554-3.3932-1.33020.391-0.6302-0.2771-1.6450.4331-0.2619-0.35190.2926-0.02840.55070.4847-0.0749-0.21220.31630.27581.248794.6591-32.802371.8054
212.98470.75360.6130.2989-0.14850.23290.54210.3644-0.750.0611-0.6297-0.14250.1002-0.13330.07650.367-0.0189-0.03230.4781-0.16730.622189.6961-27.132859.2256
222.99120.77020.8188-0.3367-1.144-0.57770.55610.067-0.8574-0.2131-0.23650.49680.23920.0128-0.27450.3241-0.0178-0.16830.3215-0.37090.7378.4706-33.683650.9009
230.8329-0.34850.54773.0486-1.11630.71250.0449-0.4701-0.6645-0.199-0.16180.54110.13690.11220.12430.43260.0502-0.21390.4709-0.36890.822477.1171-30.738449.2409
244.50193.7452-1.9094-0.33940.29153.5297-0.21110.0761-1.6288-1.0289-0.37690.3979-0.2750.5732-0.25240.45330.1127-0.29650.6333-0.59630.417272.1579-21.393639.4333
250.218-0.81170.20470.6466-0.3356-0.30180.33940.4836-0.141-0.963-0.41380.739-0.5332-0.19580.06470.76980.2423-0.28910.7435-0.45550.442866.3563-17.34230.5936
26-4.06480.26781.65094.41670.61610.65490.42410.5169-0.6514-0.6377-0.37821.4398-0.1262-0.35470.06590.32020.0859-0.2750.4368-0.31550.625566.9349-26.338340.8157
275.23764.9834-3.2457-2.1399-2.74252.04740.7613-0.36181.24040.5867-0.24660.62340.936-0.771-0.29680.3886-0.0006-0.20370.8513-0.63351.046249.8304-12.902345.0989
28-0.5571-1.3805-0.426-0.00050.23961.107-0.12540.02690.2407-0.1215-0.2025-0.03920.2228-0.14290.36030.3772-0.0288-0.10420.4487-0.31710.652775.4579-20.418150.9665
295.7616.06190.10133.0097-2.20441.074-0.13240.80680.9943-1.05590.36020.90170.2237-0.3497-0.03790.33560.0279-0.20580.4177-0.29160.722156.5061-3.802942.5728
30-0.0034-1.2125-0.35332.0513-3.96461.6896-0.35670.3202-0.3598-0.06230.53871.54580.0409-0.98140.06270.43980.0022-0.25160.5781-0.53580.871554.8993-3.785651.045
310.34981.3458-0.3731.09260.30010.44230.14420.2731-0.3818-0.0774-0.29440.5315-0.0605-0.19640.19470.2096-0.0645-0.03770.3235-0.21240.355874.9473-11.087160.5859
32-2.7238-3.9577-2.04771.78421.1927-0.19440.2127-0.1377-0.4886-0.33860.4614-0.9269-0.38040.5792-0.84520.57830.08570.03781.1473-0.52411.809487.2283-23.280530.111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 77:88)A77 - 88
2X-RAY DIFFRACTION2(chain A and resid 89:124)A89 - 124
3X-RAY DIFFRACTION3(chain A and resid 125:146)A125 - 146
4X-RAY DIFFRACTION4(chain A and resid 147:159)A147 - 159
5X-RAY DIFFRACTION5(chain A and resid 160:185)A160 - 185
6X-RAY DIFFRACTION6(chain A and resid 186:221)A186 - 221
7X-RAY DIFFRACTION7(chain A and resid 222:252)A222 - 252
8X-RAY DIFFRACTION8(chain A and resid 253:264)A253 - 264
9X-RAY DIFFRACTION9(chain A and resid 265:280)A265 - 280
10X-RAY DIFFRACTION10(chain A and resid 281:314)A281 - 314
11X-RAY DIFFRACTION11(chain A and resid 315:339)A315 - 339
12X-RAY DIFFRACTION12(chain A and resid 340:372)A340 - 372
13X-RAY DIFFRACTION13(chain A and resid 373:400)A373 - 400
14X-RAY DIFFRACTION14(chain A and resid 401:448)A401 - 448
15X-RAY DIFFRACTION15(chain A and resid 449:490)A449 - 490
16X-RAY DIFFRACTION16(chain A and resid 491:496)A491 - 496
17X-RAY DIFFRACTION17(chain B and resid 77:100)B77 - 100
18X-RAY DIFFRACTION18(chain B and resid 108:116)B108 - 116
19X-RAY DIFFRACTION19(chain B and resid 117:145)B117 - 145
20X-RAY DIFFRACTION20(chain B and resid 146:159)B146 - 159
21X-RAY DIFFRACTION21(chain B and resid 160:198)B160 - 198
22X-RAY DIFFRACTION22(chain B and resid 199:220)B199 - 220
23X-RAY DIFFRACTION23(chain B and resid 221:251)B221 - 251
24X-RAY DIFFRACTION24(chain B and resid 252:264)B252 - 264
25X-RAY DIFFRACTION25(chain B and resid 265:296)B265 - 296
26X-RAY DIFFRACTION26(chain B and resid 297:329)B297 - 329
27X-RAY DIFFRACTION27(chain B and resid 330:340)B330 - 340
28X-RAY DIFFRACTION28(chain B and resid 341:375)B341 - 375
29X-RAY DIFFRACTION29(chain B and resid 376:397)B376 - 397
30X-RAY DIFFRACTION30(chain B and resid 398:421)B398 - 421
31X-RAY DIFFRACTION31(chain B and resid 422:490)B422 - 490
32X-RAY DIFFRACTION32(chain B and resid 491:496)B491 - 496

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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