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- PDB-3hls: Crystal structure of the signaling helix coiled-coil doimain of t... -

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Basic information

Entry
Database: PDB / ID: 3hls
TitleCrystal structure of the signaling helix coiled-coil doimain of the BETA-1 subunit of the soluble guanylyl cyclase
ComponentsGuanylate cyclase soluble subunit beta-1
KeywordsSIGNALING PROTEIN / coiled-coil domain / signaling helix / S-helix / cGMP biosynthesis / Cytoplasm / GTP-binding / Heme / Iron / Lyase / Metal-binding / Nucleotide-binding
Function / homology
Function and homology information


Smooth Muscle Contraction / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase complex, soluble / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / presynaptic active zone cytoplasmic component / response to oxygen levels / nitric oxide binding / cGMP-mediated signaling ...Smooth Muscle Contraction / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase complex, soluble / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / presynaptic active zone cytoplasmic component / response to oxygen levels / nitric oxide binding / cGMP-mediated signaling / presynaptic active zone / cellular response to nitric oxide / nitric oxide-cGMP-mediated signaling / Hsp90 protein binding / glutamatergic synapse / heme binding / protein-containing complex binding / GTP binding / protein-containing complex / metal ion binding / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #780 / Haem NO binding associated / Haem NO binding associated domain superfamily / Heme NO binding associated / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / NO signalling/Golgi transport ligand-binding domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #780 / Haem NO binding associated / Haem NO binding associated domain superfamily / Heme NO binding associated / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / NO signalling/Golgi transport ligand-binding domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Guanylate cyclase soluble subunit beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsMa, X. / van den Akker, F.
CitationJournal: Bmc Struct.Biol. / Year: 2010
Title: Crystal structure of the signaling helix coiled-coil domain of the beta-1 subunit of the soluble guanylyl cyclase.
Authors: Ma, X. / Beuve, A. / van den Akker, F.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate cyclase soluble subunit beta-1
B: Guanylate cyclase soluble subunit beta-1
C: Guanylate cyclase soluble subunit beta-1
D: Guanylate cyclase soluble subunit beta-1
E: Guanylate cyclase soluble subunit beta-1
F: Guanylate cyclase soluble subunit beta-1
G: Guanylate cyclase soluble subunit beta-1
H: Guanylate cyclase soluble subunit beta-1


Theoretical massNumber of molelcules
Total (without water)62,5498
Polymers62,5498
Non-polymers00
Water8,287460
1
A: Guanylate cyclase soluble subunit beta-1
B: Guanylate cyclase soluble subunit beta-1


Theoretical massNumber of molelcules
Total (without water)15,6372
Polymers15,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-24 kcal/mol
Surface area10280 Å2
MethodPISA
2
C: Guanylate cyclase soluble subunit beta-1
D: Guanylate cyclase soluble subunit beta-1


Theoretical massNumber of molelcules
Total (without water)15,6372
Polymers15,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-25 kcal/mol
Surface area9660 Å2
MethodPISA
3
E: Guanylate cyclase soluble subunit beta-1
F: Guanylate cyclase soluble subunit beta-1


Theoretical massNumber of molelcules
Total (without water)15,6372
Polymers15,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-23 kcal/mol
Surface area9780 Å2
MethodPISA
4
G: Guanylate cyclase soluble subunit beta-1
H: Guanylate cyclase soluble subunit beta-1


Theoretical massNumber of molelcules
Total (without water)15,6372
Polymers15,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-25 kcal/mol
Surface area9650 Å2
MethodPISA
5
A: Guanylate cyclase soluble subunit beta-1
B: Guanylate cyclase soluble subunit beta-1
C: Guanylate cyclase soluble subunit beta-1
D: Guanylate cyclase soluble subunit beta-1


Theoretical massNumber of molelcules
Total (without water)31,2754
Polymers31,2754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-95 kcal/mol
Surface area13700 Å2
MethodPISA
6
E: Guanylate cyclase soluble subunit beta-1
F: Guanylate cyclase soluble subunit beta-1
G: Guanylate cyclase soluble subunit beta-1
H: Guanylate cyclase soluble subunit beta-1


Theoretical massNumber of molelcules
Total (without water)31,2754
Polymers31,2754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-95 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.039, 65.814, 98.626
Angle α, β, γ (deg.)90.00, 129.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Guanylate cyclase soluble subunit beta-1 / GCS-beta-1 / Soluble guanylate cyclase small subunit


Mass: 7818.653 Da / Num. of mol.: 8 / Fragment: Coiled-coil domain / Mutation: I371M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Guc1b3, Gucy1b1, Gucy1b3, soluble guanylyl cyclase beta-1
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P20595, guanylate cyclase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris pH 7.0, 0.7M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2008
RadiationMonochromator: vertically focusing mirror and a horizontally focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.15→39.81 Å / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.082 / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.15→39.81 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.172 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26113 2023 5 %RANDOM
Rwork0.21326 ---
obs0.21568 38302 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 0 460 4612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224194
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2112.0225648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0225498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64124.356202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97215864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3571540
X-RAY DIFFRACTIONr_chiral_restr0.080.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023012
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22032
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2870.22898
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2356
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.53222625
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.75334090
X-RAY DIFFRACTIONr_scbond_it3.34421730
X-RAY DIFFRACTIONr_scangle_it5.17531558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 139 -
Rwork0.221 2586 -
obs-2725 91.38 %

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