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- PDB-1ykd: Crystal Structure of the Tandem GAF Domains from a Cyanobacterial... -

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Basic information

Entry
Database: PDB / ID: 1ykd
TitleCrystal Structure of the Tandem GAF Domains from a Cyanobacterial Adenylyl Cyclase: Novel Modes of Ligand-Binding and Dimerization
Componentsadenylate cyclaseAdenylyl cyclase
KeywordsLYASE / gaf domain / bound cyclic AMP ligand
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / adenylate cyclase / adenylate cyclase activity / intracellular signal transduction / nucleotide binding
Similarity search - Function
PAS domain / Adenylyl- / guanylyl cyclase, catalytic domain / GAF domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain ...PAS domain / Adenylyl- / guanylyl cyclase, catalytic domain / GAF domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Adenylate cyclase
Similarity search - Component
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsMartinez, S.E. / Bruder, S. / Schultz, A. / Zheng, N. / Schultz, J.E. / Beavo, J.A. / Linder, J.U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal structure of the tandem GAF domains from a cyanobacterial adenylyl cyclase: Modes of ligand binding and dimerization
Authors: Martinez, S.E. / Bruder, S. / Schultz, A. / Zheng, N. / Schultz, J.E. / Beavo, J.A. / Linder, J.U.
History
DepositionJan 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: adenylate cyclase
B: adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1746
Polymers89,8572
Non-polymers1,3174
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-79 kcal/mol
Surface area36650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.958, 66.265, 70.212
Angle α, β, γ (deg.)103.57, 96.56, 115.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein adenylate cyclase / Adenylyl cyclase


Mass: 44928.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Gene: cyaB2
Plasmid: cloned into Qiagen plasmid pQE-60 at the NcoI-BamH1 sites
Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21(DE3) / References: UniProt: P94182, adenylate cyclase
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: ammonium sulfate, bis-tris propane, glycerol, Tris, MgCl2, betamercaptoethanol, 3',5' cyclic adenosine monophosphate, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2003
RadiationMonochromator: Si (220), single crystal, cylindrically bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.2 Å / Num. obs: 74903 / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.2 Å2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→48.2 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.55 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21532 3550 5.1 %RANDOM
Rwork0.18234 ---
obs0.18401 66116 93.04 %-
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: 20.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.88 Å21.03 Å2
2---0.26 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6031 0 88 475 6594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226251
X-RAY DIFFRACTIONr_bond_other_d0.0020.025599
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.9828479
X-RAY DIFFRACTIONr_angle_other_deg0.731313090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455760
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_restr0.0620.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021176
X-RAY DIFFRACTIONr_nbd_refined0.1850.21167
X-RAY DIFFRACTIONr_nbd_other0.2210.26298
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.23607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2372
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.27433811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37556153
X-RAY DIFFRACTIONr_scbond_it2.99672440
X-RAY DIFFRACTIONr_scangle_it4.885102326
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.952 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 207
Rwork0.279 4125
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)
11.6171-0.95120.05314.53365.20726.78140.12710.04880.0351-0.6012-0.007-0.159-0.94170.0995-0.12010.2844-0.00060.06680.03320.03120.0453-4.933313.00736.4568
20.6559-0.3086-0.2891.05920.15140.23070.0316-0.0608-0.0802-0.0524-0.0292-0.0028-0.0352-0.021-0.00250.09650.0145-0.02940.1579-0.01340.126510.7063-20.6493-2.1343
30.61540.55130.07840.5689-0.06240.2450.1035-0.07990.0075-0.00040.00160.0127-0.0234-0.0228-0.10510.1262-0.0182-0.01270.1494-0.00630.1246-21.3429-8.565122.2102
41.9651-1.0146-1.23371.50272.13912.12720.09160.0476-0.1467-0.1005-0.10350.1387-0.1791-0.04920.01190.1740.0269-0.00650.1241-0.02590.1109-9.64012.23746.2135
50.13150.3885-0.08720.4922-0.00210.8989-0.0591-0.0104-0.04540.0099-0.07110.00190.00790.09380.13020.12660.0337-0.00350.14020.02330.12290.542122.250636.5727
60.23520.47970.11890.8688-0.09810.3974-0.07450.08580.03180.1272-0.0529-0.0340.08460.05020.12740.13830.0280.02360.10880.00730.145516.457218.794-2.1043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA58 - 771 - 20
2X-RAY DIFFRACTION2AA78 - 24621 - 189
3X-RAY DIFFRACTION2AC5011
4X-RAY DIFFRACTION3AA247 - 440190 - 383
5X-RAY DIFFRACTION3AD5021
6X-RAY DIFFRACTION4BB58 - 771 - 20
7X-RAY DIFFRACTION5BB78 - 24621 - 189
8X-RAY DIFFRACTION5BE5031
9X-RAY DIFFRACTION6BB247 - 441190 - 384
10X-RAY DIFFRACTION6BF5041

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