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- PDB-2wz1: STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN SOLUBLE GUANYLATE CYCL... -

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Basic information

Entry
Database: PDB / ID: 2wz1
TitleSTRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN SOLUBLE GUANYLATE CYCLASE 1 BETA 3.
ComponentsGUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1
KeywordsLYASE / GUCY1 / METAL-BINDING / CGMP BIOSYNTHESIS / NUCLEOTIDE-BINDING / CYCLASE / GUCY1B3 / GTP-BINDING
Function / homology
Function and homology information


cytidylate cyclase activity / guanylate cyclase complex, soluble / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / response to oxygen levels / presynaptic active zone cytoplasmic component / Nitric oxide stimulates guanylate cyclase / adenylate cyclase activity ...cytidylate cyclase activity / guanylate cyclase complex, soluble / trans-synaptic signaling by nitric oxide, modulating synaptic transmission / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / response to oxygen levels / presynaptic active zone cytoplasmic component / Nitric oxide stimulates guanylate cyclase / adenylate cyclase activity / blood circulation / nitric oxide-cGMP-mediated signaling / cGMP-mediated signaling / Smooth Muscle Contraction / cellular response to nitric oxide / nitric oxide mediated signal transduction / Hsp90 protein binding / signaling receptor activity / glutamatergic synapse / heme binding / protein-containing complex binding / GTP binding / metal ion binding / cytosol
Similarity search - Function
Haem NO binding associated domain superfamily / Haem NO binding associated / Heme NO binding associated / Nucleotide cyclase, GGDEF domain / 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 ...Haem NO binding associated domain superfamily / Haem NO binding associated / Heme NO binding associated / Nucleotide cyclase, GGDEF domain / 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 / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Guanylate cyclase soluble subunit beta-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsAllerston, C.K. / Cooper, C.D.O. / Muniz, J. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structures of the Catalytic Domain of Human Soluble Guanylate Cyclase.
Authors: Allerston, C.K. / von Delft, F. / Gileadi, O.
History
DepositionNov 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 10, 2013Group: Database references / Derived calculations / Refinement description
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1
B: GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5005
Polymers49,3142
Non-polymers1863
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-10.7 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.590, 90.380, 140.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.94655, -0.08878, 0.3101), (0.0094, -0.96857, -0.24858), (0.32243, -0.23238, 0.91763)
Vector: -44.16552, -33.16879, 2.5419)

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Components

#1: Protein GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1 / GUANYLATE CYCLASE 1 BETA 3 / GCS-BETA-1 / SOLUBLE GUANYLATE CYCLASE SMALL SUBUNIT / GCS-BETA-3


Mass: 24657.020 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 994-1205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE2 / References: UniProt: Q02153, guanylate cyclase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.1 Å3/Da / Density % sol: 41.45 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: PROTEIN WAS CONCENTRATED TO 12 MG/ML IN PURIFICATION BUFFER (10MM HEPES, 500MM NACL, 5% GLYCEROL, 10% GALACTOSE, 0.5MM TCEP)AND SET UP IN SITTING DROP IN A 1:2 RATIO WITH HAMPTON INDEX ...Details: PROTEIN WAS CONCENTRATED TO 12 MG/ML IN PURIFICATION BUFFER (10MM HEPES, 500MM NACL, 5% GLYCEROL, 10% GALACTOSE, 0.5MM TCEP)AND SET UP IN SITTING DROP IN A 1:2 RATIO WITH HAMPTON INDEX SCREEN - B8 (1.4M TRI-SODIUM CITRATE DIHYDRATE, 0.1M HEPES, PH 7.5).

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→37 Å / Num. obs: 49220 / % possible obs: 99.3 % / Observed criterion σ(I): 1.3 / Redundancy: 3.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ET6

3et6


Resolution: 1.63→37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.37 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21922 2637 5.1 %RANDOM
Rwork0.18352 ---
obs0.18536 49220 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.388 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.63→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 12 289 3357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223207
X-RAY DIFFRACTIONr_bond_other_d0.0010.022197
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9554331
X-RAY DIFFRACTIONr_angle_other_deg1.23835374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95423.453139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65915570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8311522
X-RAY DIFFRACTIONr_chiral_restr0.0990.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213506
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02642
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.74231974
X-RAY DIFFRACTIONr_mcbond_other1.1313805
X-RAY DIFFRACTIONr_mcangle_it5.45253224
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.71581233
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.01121106
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 180 -
Rwork0.302 3626 -
obs--99.84 %
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)
12.21560.19970.41691.88880.17732.12820.02640.00140.0066-0.02350.0086-0.15880.03260.189-0.03490.00750.00530.00120.0206-0.00290.014-37.1526-10.7107-13.8246
22.39640.0686-0.07392.0511-0.05722.8682-0.0623-0.0783-0.07860.1698-0.00190.16990.1244-0.12750.06420.0406-0.01760.01460.03460.00360.0198-12.1851-19.6296-19.6586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A412 - 610
2X-RAY DIFFRACTION2B412 - 608

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