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- PDB-4gj4: The Crystal Structure of the soluble Guanylate Cyclase PAS alpha ... -

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Basic information

Entry
Database: PDB / ID: 4gj4
TitleThe Crystal Structure of the soluble Guanylate Cyclase PAS alpha domain from Manduca sexta
ComponentsSoluble guanylyl cyclase alpha-1 subunit
KeywordsLYASE / Nitric Oxide / cGMP / YC-1 / PAS Domain / PAS Fold / Allosteric Regulation
Function / homology
Function and homology information


guanylate cyclase / guanylate cyclase activity / intracellular signal transduction / heme binding / GTP binding / cytoplasm
Similarity search - Function
Haem NO binding associated domain / Haem NO binding associated domain superfamily / Haem NO binding associated / 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 ...Haem NO binding associated domain / Haem NO binding associated domain superfamily / Haem NO binding associated / 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 / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesManduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPurohit, R. / Montfort, W.R. / Weichsel, A.
CitationJournal: Protein Sci. / Year: 2013
Title: Crystal structure of the Alpha subunit PAS domain from soluble guanylyl cyclase.
Authors: Purohit, R. / Weichsel, A. / Montfort, W.R.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Soluble guanylyl cyclase alpha-1 subunit
B: Soluble guanylyl cyclase alpha-1 subunit
C: Soluble guanylyl cyclase alpha-1 subunit
D: Soluble guanylyl cyclase alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,34115
Polymers55,2854
Non-polymers1,05711
Water2,972165
1
A: Soluble guanylyl cyclase alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9172
Polymers13,8211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble guanylyl cyclase alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1094
Polymers13,8211
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Soluble guanylyl cyclase alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2055
Polymers13,8211
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Soluble guanylyl cyclase alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1094
Polymers13,8211
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Soluble guanylyl cyclase alpha-1 subunit
B: Soluble guanylyl cyclase alpha-1 subunit
C: Soluble guanylyl cyclase alpha-1 subunit
D: Soluble guanylyl cyclase alpha-1 subunit
hetero molecules

A: Soluble guanylyl cyclase alpha-1 subunit
B: Soluble guanylyl cyclase alpha-1 subunit
C: Soluble guanylyl cyclase alpha-1 subunit
D: Soluble guanylyl cyclase alpha-1 subunit
hetero molecules

A: Soluble guanylyl cyclase alpha-1 subunit
B: Soluble guanylyl cyclase alpha-1 subunit
C: Soluble guanylyl cyclase alpha-1 subunit
D: Soluble guanylyl cyclase alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,02445
Polymers165,85412
Non-polymers3,17033
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area27490 Å2
ΔGint-558 kcal/mol
Surface area57170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.424, 95.424, 317.693
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Soluble guanylyl cyclase alpha-1 subunit


Mass: 13821.136 Da / Num. of mol.: 4 / Fragment: sGC PAS alpha Domain residues 279-404 / Mutation: C285A, C352A, C374A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: O77105, guanylate cyclase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.5 M Lithium Sulfate, 0.1 M Hepes, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 7, 2012 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→23.7 Å / Num. all: 52047 / Num. obs: 52047 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.75 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.56 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5122 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345325data collection
MrBUMPphasing
REFMAC5.6.0117refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P04

2p04


Resolution: 1.8→23.15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.651 / SU ML: 0.098 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 2658 5.1 %RANDOM
Rwork0.1962 ---
obs0.19845 49385 99.88 %-
all-52047 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.294 Å
Refinement stepCycle: LAST / Resolution: 1.8→23.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 55 165 3756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193762
X-RAY DIFFRACTIONr_bond_other_d0.0010.022629
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9895089
X-RAY DIFFRACTIONr_angle_other_deg0.90436338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58321.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23215618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5371532
X-RAY DIFFRACTIONr_chiral_restr0.090.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 210 -
Rwork0.398 3324 -
obs-3324 100 %
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)
11.72320.0406-0.22172.2424-0.27132.1976-0.06210.04010.07330.09030.09280.0298-0.251-0.1563-0.03080.10120.0374-0.0210.04020.03460.0747-16.487-28.76527.215
21.42330.28370.10631.72170.26241.9612-0.0494-0.0138-0.0382-0.23910.08450.0117-0.12480.0247-0.03510.093-0.02850.01520.01460.00580.022412.238-26.57124.605
32.3010.06710.08991.8226-0.52662.57660.0287-0.06840.03270.18260.01080.1741-0.0335-0.1589-0.03950.03020.0130.01550.0284-0.00310.0174-15.767-49.81352.958
42.9483-0.6365-0.22911.61960.73452.16710.11090.43290.2034-0.1896-0.06680.1034-0.1092-0.1746-0.04410.15080.02-0.02060.12050.0620.0461-3.877-35.6592.886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 391
2X-RAY DIFFRACTION2B279 - 390
3X-RAY DIFFRACTION3C279 - 391
4X-RAY DIFFRACTION4D279 - 395

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