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- PDB-3hvw: Crystal Structure of the GGDEF domain of the PA2567 protein from ... -

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Basic information

Entry
Database: PDB / ID: 3hvw
TitleCrystal Structure of the GGDEF domain of the PA2567 protein from Pseudomonas aeruginosa, Northeast Structural Genomics Consortium Target PaR365C
ComponentsDiguanylate-cyclase (DGC)
KeywordsLYASE / alpha-beta protein. / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain / Nucleotide cyclase / GAF domain ...Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
EAL domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Nair, R. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target PaR365C
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diguanylate-cyclase (DGC)


Theoretical massNumber of molelcules
Total (without water)20,0951
Polymers20,0951
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.374, 53.757, 76.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diguanylate-cyclase (DGC)


Mass: 20094.611 Da / Num. of mol.: 1 / Fragment: GGDEF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2567 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9I0R8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 277 K / Method: microbatch, under oil / pH: 8
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 100mM TRIS (pH 8) and 800mM Ammonium Sulfate, microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 1, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 43513 / Num. obs: 43035 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.028 / Rsym value: 0.027 / Net I/σ(I): 49.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 23.7 / Num. unique all: 4349 / Rsym value: 0.073 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→18.18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1081506.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2143 5 %RANDOM
Rwork0.201 ---
all0.203 43396 --
obs0.202 42442 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.181 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å20 Å2
2--0.44 Å20 Å2
3----2.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.7→18.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 0 235 1495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.251 208 5 %
Rwork0.205 3974 -
obs-4182 96.7 %

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