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- PDB-2p08: Structure of the N-terminally truncated PAS domain of signal tran... -

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Basic information

Entry
Database: PDB / ID: 2p08
TitleStructure of the N-terminally truncated PAS domain of signal transduction histidine kinase from Nostoc punctiforme PCC 73102 with homology to the H-NOXA/H-NOBA domain of the soluble guanylyl cyclase
Componentssignal transduction histidine kinase
KeywordsTRANSFERASE / PAS-like domain / homologous to domain in soluble guanylyl cyclase
Function / homology
Function and homology information


guanylate cyclase / guanylate cyclase activity
Similarity search - Function
Haem NO binding associated domain / Haem NO binding associated / Haem NO binding associated domain superfamily / Heme NO binding associated / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
Authorsvan den Akker, F. / Ma, X.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure.
Authors: Ma, X. / Sayed, N. / Baskaran, P. / Beuve, A. / van den Akker, F.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: signal transduction histidine kinase
B: signal transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6974
Polymers26,5052
Non-polymers1922
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.332, 72.332, 169.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein signal transduction histidine kinase


Mass: 13252.516 Da / Num. of mol.: 2
Fragment: Delta-7 N-terminally truncated H-NOXA/H-NOBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: COG0642 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: D0VWX6*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 1.7-1.9M NH4SO4, 100mM TrisHCl pH 7.7-9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.2398
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2→35.4 Å / Num. obs: 17432 / % possible obs: 99.43 % / Redundancy: 5.68 % / Rsym value: 0.08 / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→35.36 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.948 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27802 941 5.1 %RANDOM
Rwork0.23855 ---
obs0.24056 17432 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.529 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 10 111 1892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.982473
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49824.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12815326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7111510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021378
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2763
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21237
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.17621134
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.04441777
X-RAY DIFFRACTIONr_scbond_it8.5964782
X-RAY DIFFRACTIONr_scangle_it11.6426696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 74 -
Rwork0.315 1243 -
obs--99.55 %

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