- PDB-5g0n: Structure of rat neuronal nitric oxide synthase D597N mutant heme... -
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Basic information
Entry
Database: PDB / ID: 5g0n
Title
Structure of rat neuronal nitric oxide synthase D597N mutant heme domain in complex with N1-(5-(2-(6-AMINO-4-METHYLPYRIDIN-2-YL)ETHYL) PYRIDIN-3-YL)-N1,N2-DIMETHYLETHANE-1,2-DIAMINE
Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis / positive regulation of sodium ion transmembrane transport ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis / positive regulation of sodium ion transmembrane transport / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / response to nitric oxide / postsynaptic specialization, intracellular component / nitric oxide metabolic process / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / behavioral response to cocaine / postsynaptic density, intracellular component / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / calyx of Held / negative regulation of calcium ion transport / negative regulation of serotonin uptake / sodium channel regulator activity / regulation of neurogenesis / striated muscle contraction / negative regulation of insulin secretion / response to vitamin E / nitric-oxide synthase (NADPH) / regulation of postsynaptic membrane potential / multicellular organismal response to stress / xenobiotic catabolic process / nitric-oxide synthase activity / negative regulation of peptidyl-serine phosphorylation / nitric oxide mediated signal transduction / arginine catabolic process / NADPH binding / regulation of sodium ion transport / response to organonitrogen compound / cellular response to epinephrine stimulus / sarcoplasmic reticulum membrane / T-tubule / photoreceptor inner segment / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / response to nutrient levels / response to activity / response to nicotine / sarcoplasmic reticulum / muscle contraction / secretory granule / female pregnancy / positive regulation of long-term synaptic potentiation / cell periphery / establishment of localization in cell / phosphoprotein binding / response to lead ion / sarcolemma / establishment of protein localization / potassium ion transport / response to organic cyclic compound / response to peptide hormone / cellular response to growth factor stimulus / Z disc / vasodilation / cellular response to mechanical stimulus / response to estrogen / calcium-dependent protein binding / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / ATPase binding / response to heat / scaffold protein binding / response to ethanol / nuclear membrane / negative regulation of neuron apoptotic process / mitochondrial outer membrane / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia / cytoskeleton / calmodulin binding / membrane raft / negative regulation of cell population proliferation / dendrite / glutamatergic synapse / synapse / heme binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / 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 / 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)
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Non-polymers , 6 types, 507 molecules
#2: Chemical
ChemComp-HEM / PROTOPORPHYRINIXCONTAININGFE / HEME / Heme B
Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.127 Å / Relative weight: 1
Reflection
Resolution: 1.94→50 Å / Num. obs: 70703 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 28.95 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.1
Reflection shell
Resolution: 1.94→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.1 / % possible all: 93.4
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
Aimless
datascaling
REFMAC
phasing
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.936→38.828 Å / SU ML: 0.28 / σ(F): 1.13 / Phase error: 24.76 / Stereochemistry target values: ML Details: RESIDUES 339-349 IN CHAIN A AND 339-347 IN CHAIN B ARE DISORDERED.
Rfactor
Num. reflection
% reflection
Rfree
0.2157
6676
5 %
Rwork
0.1753
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-
obs
0.1773
134166
99.23 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.936→38.828 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6659
0
173
498
7330
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
7069
X-RAY DIFFRACTION
f_angle_d
1.141
9618
X-RAY DIFFRACTION
f_dihedral_angle_d
15.182
2574
X-RAY DIFFRACTION
f_chiral_restr
0.074
994
X-RAY DIFFRACTION
f_plane_restr
0.005
1217
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9358-1.9577
0.4059
190
0.3743
3487
X-RAY DIFFRACTION
82
1.9577-1.9808
0.3815
248
0.3423
4204
X-RAY DIFFRACTION
99
1.9808-2.0049
0.4145
207
0.3191
4303
X-RAY DIFFRACTION
100
2.0049-2.0303
0.2804
203
0.287
4250
X-RAY DIFFRACTION
100
2.0303-2.057
0.2968
226
0.2794
4259
X-RAY DIFFRACTION
100
2.057-2.0852
0.3465
238
0.2741
4284
X-RAY DIFFRACTION
100
2.0852-2.115
0.3446
177
0.2695
4300
X-RAY DIFFRACTION
100
2.115-2.1466
0.2744
203
0.2469
4321
X-RAY DIFFRACTION
100
2.1466-2.1801
0.3308
198
0.2535
4294
X-RAY DIFFRACTION
100
2.1801-2.2158
0.3332
228
0.2406
4290
X-RAY DIFFRACTION
100
2.2158-2.254
0.2612
238
0.2312
4307
X-RAY DIFFRACTION
100
2.254-2.295
0.2651
259
0.2175
4193
X-RAY DIFFRACTION
100
2.295-2.3392
0.2338
244
0.2097
4257
X-RAY DIFFRACTION
100
2.3392-2.3869
0.2485
220
0.2025
4303
X-RAY DIFFRACTION
100
2.3869-2.4388
0.264
195
0.2077
4290
X-RAY DIFFRACTION
100
2.4388-2.4955
0.3117
214
0.2048
4289
X-RAY DIFFRACTION
100
2.4955-2.5579
0.2586
236
0.1935
4258
X-RAY DIFFRACTION
100
2.5579-2.6271
0.228
226
0.1839
4274
X-RAY DIFFRACTION
100
2.6271-2.7043
0.2363
210
0.172
4316
X-RAY DIFFRACTION
100
2.7043-2.7916
0.2056
204
0.1649
4274
X-RAY DIFFRACTION
100
2.7916-2.8913
0.2029
241
0.1682
4311
X-RAY DIFFRACTION
100
2.8913-3.0071
0.2065
231
0.1707
4218
X-RAY DIFFRACTION
100
3.0071-3.1439
0.2573
241
0.175
4286
X-RAY DIFFRACTION
100
3.1439-3.3095
0.2146
205
0.1645
4279
X-RAY DIFFRACTION
100
3.3095-3.5168
0.1736
214
0.1511
4306
X-RAY DIFFRACTION
100
3.5168-3.7881
0.2025
259
0.1337
4264
X-RAY DIFFRACTION
100
3.7881-4.1689
0.1717
213
0.1206
4266
X-RAY DIFFRACTION
100
4.1689-4.7712
0.1382
244
0.1173
4282
X-RAY DIFFRACTION
100
4.7712-6.0076
0.1829
253
0.1361
4223
X-RAY DIFFRACTION
100
6.0076-38.8355
0.1381
211
0.1523
4302
X-RAY DIFFRACTION
100
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
0.612
-0.0552
-0.3669
0.8352
-0.2531
3.9867
-0.0595
0.1107
-0.0223
0.0121
-0.0244
0.032
-0.0228
-0.2997
0.0572
0.1632
-0.0225
-0.0006
0.2067
-0.0153
0.1905
11.3816
4.8823
22.4398
2
0.661
-0.1217
-0.1222
0.8418
0.3578
2.0437
-0.0173
-0.0017
0.0496
-0.0839
-0.035
-0.0175
0.0118
0.0742
0.0497
0.1347
0.0043
0.0162
0.1449
0.013
0.1872
12.094
4.8045
59.7331
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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