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- PDB-3lyx: Crystal structure of the PAS domain of the protein CPS_1291 from ... -

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Basic information

Entry
Database: PDB / ID: 3lyx
TitleCrystal structure of the PAS domain of the protein CPS_1291 from Colwellia psychrerythraea. Northeast Structural Genomics Consortium target id CsR222B
ComponentsSensory box/GGDEF domain protein
KeywordsTRANSCRIPTION / sensory box-GGDEF domain protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase ...: / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sensory box/GGDEF domain protein
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSeetharaman, J. / Chen, Y. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Chen, Y. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the PAS domain of the protein CPS_1291 from Colwellia psychrerythraea. Northeast Structural Genomics Consortium target id CsR222B
Authors: Seetharaman, J. / Chen, Y. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensory box/GGDEF domain protein
B: Sensory box/GGDEF domain protein


Theoretical massNumber of molelcules
Total (without water)28,1182
Polymers28,1182
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-17 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.873, 51.873, 155.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Sensory box/GGDEF domain protein


Mass: 14059.006 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: CPS_1291 / Production host: Escherichia coli (E. coli) / References: UniProt: Q486I1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: KBr 0.1 M, HEPES 0.1 M (pH 7.5), PEG 8000 40%, glycerol 10%, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 30613 / Num. obs: 30613 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.058 / Net I/σ(I): 23.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 22 / Num. unique all: 1459 / Rsym value: 0.42 / % possible all: 93.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→43.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 149406.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1646 5.9 %RANDOM
Rwork0.225 ---
obs0.225 28116 88.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7646 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 0 141 2028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 245 6.6 %
Rwork0.257 3483 -
obs--71.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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