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- PDB-2p04: 2.1 Ang structure of the dimerized PAS domain of signal transduct... -

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Basic information

Entry
Database: PDB / ID: 2p04
Title2.1 Ang structure of the dimerized 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 kinaseTwo-component regulatory system
KeywordsTRANSFERASE / PAS-like fold dimer / homologous to soluble guanylyl cyclase domain
Function / homology
Function and homology information


guanylate cyclase / guanylate cyclase activity / nucleotide binding
Similarity search - Function
Haem NO binding associated domain / Haem NO binding associated domain superfamily / Haem NO binding associated / Heme NO binding associated / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)27,7402
Polymers27,7402
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-17 kcal/mol
Surface area10870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.210, 44.362, 59.740
Angle α, β, γ (deg.)90.00, 104.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein signal transduction histidine kinase / Two-component regulatory system


Mass: 13870.230 Da / Num. of mol.: 2 / Fragment: 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: D0VWX5*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 1.5M LiSO4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 12364 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.119 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.456 / % possible all: 59.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Truncated delta-7 H-NOXA structure

Resolution: 2.11→25.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.062 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.262 614 5 %RANDOM
Rwork0.19928 ---
obs0.20232 11666 86.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.334 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.11→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 0 55 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9782410
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1452485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05115315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5591510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021360
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2780
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21219
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.592.51110
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.913.51739
X-RAY DIFFRACTIONr_scbond_it4.743751
X-RAY DIFFRACTIONr_scangle_it6.6444.5671
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.11 Å / Num. reflection Rwork: 556 / Total num. of bins used: 20

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