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- PDB-3gof: Calmodulin bound to peptide from macrophage nitric oxide synthase -

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Basic information

Entry
Database: PDB / ID: 3gof
TitleCalmodulin bound to peptide from macrophage nitric oxide synthase
Components
  • Calmodulin
  • Nitric oxide synthase, inducible
KeywordsMETAL BINDING PROTEIN/OXIDOREDUCTASE / PROTEIN-PEPTIDE COMPLEX / METAL BINDING PROTEIN / Acetylation / Calcium / Methylation / Calmodulin-binding / FAD / FMN / Heme / Iron / Metal-binding / NADP / Oxidoreductase / Polymorphism / Zinc / METAL BINDING PROTEIN-OXIDOREDUCTASE COMPLEX
Function / homology
Function and homology information


CH domain binding / 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 / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding ...CH domain binding / 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 / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding / myosin binding / cortical cytoskeleton / superoxide metabolic process / cGMP-mediated signaling / nitric-oxide synthase binding / cellular response to cytokine stimulus / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / regulation of insulin secretion / cellular response to organic cyclic compound / nitric-oxide synthase (NADPH) / blood vessel remodeling / response to tumor necrosis factor / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / positive regulation of interleukin-8 production / response to bacterium / Hsp90 protein binding / negative regulation of protein catabolic process / beta-catenin binding / regulation of blood pressure / peroxisome / positive regulation of interleukin-6 production / cellular response to type II interferon / circadian rhythm / disordered domain specific binding / cellular response to xenobiotic stimulus / FMN binding / flavin adenine dinucleotide binding / NADP binding / actin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / response to hypoxia / calmodulin binding / intracellular signal transduction / defense response to bacterium / cadherin binding / inflammatory response / positive regulation of apoptotic process / negative regulation of gene expression / calcium ion binding / heme binding / protein kinase binding / perinuclear region of cytoplasm / protein homodimerization activity / protein-containing complex / extracellular space / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / EF-hand / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding ...Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / EF-hand / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Recoverin; domain 1 / 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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nitric oxide synthase, inducible / Calmodulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsNg, H.L. / Greenstein, A. / Marletta, M. / Wand, A.J. / Alber, T.
CitationJournal: To be Published
Title: Structural diversity in calmodulin recognition of nitric oxide synthases
Authors: Ng, H.L. / Greenstein, A. / Marletta, M. / Wand, A.J. / Alber, T.
History
DepositionMar 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Calmodulin
C: Nitric oxide synthase, inducible
D: Nitric oxide synthase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,20914
Polymers37,6964
Non-polymers51310
Water9,206511
1
A: Calmodulin
C: Nitric oxide synthase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1047
Polymers18,8482
Non-polymers2565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-79 kcal/mol
Surface area8850 Å2
MethodPISA
2
B: Calmodulin
D: Nitric oxide synthase, inducible
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1047
Polymers18,8482
Non-polymers2565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-81 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.923, 57.773, 60.231
Angle α, β, γ (deg.)90.00, 93.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin / / CaM


Mass: 16721.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALM, CAM, RCJMB04_24e7 / Production host: Escherichia coli (E. coli) / References: UniProt: P62149
#2: Protein/peptide Nitric oxide synthase, inducible / / Inducible NO synthase / Inducible NOS / iNOS / NOS type II / Macrophage NOS / MAC-NOS


Mass: 2126.638 Da / Num. of mol.: 2 / Fragment: Calcium binding domain / Source method: obtained synthetically
Details: The peptide is naturally found in Mus musculus (mouse).
References: UniProt: P29477, nitric-oxide synthase (NADPH)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0332 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.45→60 Å / Num. obs: 52623 / % possible obs: 97 % / Redundancy: 3.7 % / Rsym value: 0.071
Reflection shellResolution: 1.45→1.52 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.329 / % possible all: 95.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.45→9.34 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.133 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20822 2687 5.1 %RANDOM
Rwork0.14482 ---
obs0.14802 50255 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.07 Å2
2--1.24 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.45→9.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 18 511 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222690
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9623599
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6295318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21475
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2344
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.232
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.04651593
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.13862575
X-RAY DIFFRACTIONr_scbond_it5.67961097
X-RAY DIFFRACTIONr_scangle_it7.3267.51024
X-RAY DIFFRACTIONr_rigid_bond_restr2.19322690
X-RAY DIFFRACTIONr_sphericity_free12.2955519
X-RAY DIFFRACTIONr_sphericity_bonded8.17352662
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 179
Rwork0.167 3652

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