- PDB-5g0o: Structure of rat neuronal nitric oxide synthase D597N mutant heme... -
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Basic information
Entry
Database: PDB / ID: 5g0o
Title
Structure of rat neuronal nitric oxide synthase D597N mutant heme domain in complex with 4-METHYL-6-(2-(5-(4-METHYLPIPERAZIN-1-YL) PYRIDIN-3-YL)ETHYL)PYRIDIN-2-AMINE
Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport / response to nitric oxide / nitric oxide metabolic process / postsynaptic specialization, intracellular component / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Ion homeostasis / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / negative regulation of calcium ion transport / calyx of Held / behavioral response to cocaine / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase (NADPH) / sodium channel regulator activity / response to vitamin E / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / negative regulation of insulin secretion / nitric oxide mediated signal transduction / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / arginine catabolic process / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / sarcoplasmic reticulum membrane / T-tubule / cellular response to epinephrine stimulus / : / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to nutrient levels / potassium ion transport / response to hormone / sarcoplasmic reticulum / secretory granule / response to activity / positive regulation of long-term synaptic potentiation / establishment of localization in cell / cell periphery / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / establishment of protein localization / cellular response to mechanical stimulus / vasodilation / response to organic cyclic compound / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / response to estrogen / calcium-dependent protein binding / calcium ion transport / positive regulation of peptidyl-serine phosphorylation / FMN binding / ATPase binding / NADP binding / flavin adenine dinucleotide binding / nuclear membrane / response to heat / scaffold protein binding / response to ethanol / negative regulation of neuron apoptotic process / transmembrane transporter binding / mitochondrial outer membrane / response to lipopolysaccharide / dendritic spine / calmodulin binding / postsynaptic density / cytoskeleton / response to hypoxia / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / synapse / dendrite / heme binding / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II Similarity search - Function
NITRICOXIDESYNTHASE, BRAIN / BNOS / CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S- ...BNOS / CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S-NITROSYLASE NOS1 / NEURONAL NITRIC OXIDE SYNTHASE
Mass: 48811.543 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, RESIDUES 297-718 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH)
Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.087 Å / Relative weight: 1
Reflection
Resolution: 1.85→50 Å / Num. obs: 81212 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 30.29 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.1
Reflection shell
Resolution: 1.85→1.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.7 / % possible all: 100
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
MOSFLM
datareduction
Aimless
datascaling
REFMAC
phasing
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.85→49.312 Å / SU ML: 0.21 / σ(F): 0.02 / Phase error: 32.88 / Stereochemistry target values: ML Details: RESIDUES 339-349 IN CHAIN A AND 339-347 IN CHAIN B ARE DISORDERED.
Rfactor
Num. reflection
% reflection
Rfree
0.2329
7652
4.9 %
Rwork
0.1931
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-
obs
0.1952
80907
99.48 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.85→49.312 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6659
0
175
460
7294
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
7078
X-RAY DIFFRACTION
f_angle_d
1.166
9635
X-RAY DIFFRACTION
f_dihedral_angle_d
14.931
2583
X-RAY DIFFRACTION
f_chiral_restr
0.073
998
X-RAY DIFFRACTION
f_plane_restr
0.005
1216
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.85-1.871
0.4073
227
0.3535
4738
X-RAY DIFFRACTION
98
1.871-1.8931
0.4448
254
0.3415
4878
X-RAY DIFFRACTION
99
1.8931-1.9161
0.3607
235
0.3421
4927
X-RAY DIFFRACTION
99
1.9161-1.9404
0.4112
254
0.3405
4855
X-RAY DIFFRACTION
100
1.9404-1.9659
0.3981
286
0.3229
4837
X-RAY DIFFRACTION
99
1.9659-1.9929
0.3915
267
0.3142
4906
X-RAY DIFFRACTION
99
1.9929-2.0213
0.3321
232
0.3049
4898
X-RAY DIFFRACTION
99
2.0213-2.0515
0.3461
265
0.3006
4881
X-RAY DIFFRACTION
99
2.0515-2.0836
0.3651
267
0.2913
4882
X-RAY DIFFRACTION
100
2.0836-2.1177
0.3746
197
0.2764
4888
X-RAY DIFFRACTION
100
2.1177-2.1542
0.3104
242
0.2697
5046
X-RAY DIFFRACTION
99
2.1542-2.1934
0.3543
224
0.2615
4864
X-RAY DIFFRACTION
100
2.1934-2.2356
0.336
260
0.2505
4919
X-RAY DIFFRACTION
100
2.2356-2.2812
0.2833
312
0.2484
4839
X-RAY DIFFRACTION
100
2.2812-2.3308
0.276
275
0.232
4902
X-RAY DIFFRACTION
100
2.3308-2.3851
0.299
242
0.2307
4912
X-RAY DIFFRACTION
100
2.3851-2.4447
0.3292
244
0.2372
4991
X-RAY DIFFRACTION
100
2.4447-2.5108
0.3243
250
0.2271
4866
X-RAY DIFFRACTION
100
2.5108-2.5847
0.2839
266
0.2062
4928
X-RAY DIFFRACTION
100
2.5847-2.6681
0.2234
240
0.208
4884
X-RAY DIFFRACTION
100
2.6681-2.7634
0.262
232
0.2046
4971
X-RAY DIFFRACTION
100
2.7634-2.8741
0.2605
270
0.2011
4922
X-RAY DIFFRACTION
100
2.8741-3.0049
0.2311
260
0.1952
4868
X-RAY DIFFRACTION
100
3.0049-3.1633
0.2479
286
0.1908
4898
X-RAY DIFFRACTION
100
3.1633-3.3614
0.222
241
0.181
4930
X-RAY DIFFRACTION
100
3.3614-3.6209
0.1919
262
0.1569
4898
X-RAY DIFFRACTION
100
3.6209-3.9851
0.1793
250
0.1427
4950
X-RAY DIFFRACTION
100
3.9851-4.5614
0.1552
276
0.1338
4867
X-RAY DIFFRACTION
100
4.5614-5.7455
0.1854
301
0.1407
4869
X-RAY DIFFRACTION
99
5.7455-49.3299
0.1519
235
0.1623
4843
X-RAY DIFFRACTION
98
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
0.9178
-0.0361
-0.5191
1.5938
-0.4282
6.4587
-0.0609
0.1291
-0.0049
0.0902
-0.0657
0.0768
0.0011
-0.3858
0.0345
0.1805
-0.0249
0.0091
0.1215
-0.0136
0.125
11.372
4.8094
22.4969
2
1.1546
-0.3178
-0.0858
1.2622
0.3738
3.6177
-0.0219
0.0309
0.0813
-0.1777
-0.0855
0.0024
-0.0096
0.1271
0.0441
0.1749
0.0216
0.0364
0.0518
0.0255
0.107
12.1791
4.7926
59.7429
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAINAANDRESID299:716)
2
X-RAY DIFFRACTION
2
(CHAINBANDRESID299:718)
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