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- PDB-3pjw: Structure of Pseudomonas fluorescence LapD GGDEF-EAL dual domain, I23 -

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Basic information

Entry
Database: PDB / ID: 3pjw
TitleStructure of Pseudomonas fluorescence LapD GGDEF-EAL dual domain, I23
ComponentsCyclic dimeric GMP binding protein
KeywordsLYASE / GGDEF-EAL tandem domain / c-di-GMP receptor
Function / homology
Function and homology information


nucleotide binding / signal transduction / identical protein binding / membrane
Similarity search - Function
LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY periplasmic domain / EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain ...LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY periplasmic domain / EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / GGDEF domain profile. / GGDEF domain / HAMP domain profile. / HAMP domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Diguanylate cyclase/phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1006 Å
AuthorsSondermann, H. / Navarro, M.V.A.S.
CitationJournal: Plos Biol. / Year: 2011
Title: Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis.
Authors: Navarro, M.V. / Newell, P.D. / Krasteva, P.V. / Chatterjee, D. / Madden, D.R. / O'Toole, G.A. / Sondermann, H.
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: 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 ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic dimeric GMP binding protein


Theoretical massNumber of molelcules
Total (without water)47,8051
Polymers47,8051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.845, 154.845, 154.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Cyclic dimeric GMP binding protein


Mass: 47804.934 Da / Num. of mol.: 1 / Fragment: UNP Residues 220-648
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: lapD, Pfl01_0131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KK31

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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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate, 15% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 11371 / Num. obs: 11246 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.1→3.29 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1006→48.966 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 539 4.8 %RANDOM
Rwork0.2338 ---
obs0.2362 11240 98.84 %-
all-11371 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.39 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1006→48.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 0 0 3315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113368
X-RAY DIFFRACTIONf_angle_d1.4054550
X-RAY DIFFRACTIONf_dihedral_angle_d21.1271254
X-RAY DIFFRACTIONf_chiral_restr0.082504
X-RAY DIFFRACTIONf_plane_restr0.007606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1006-3.41260.36981370.33762631X-RAY DIFFRACTION99
3.4126-3.90620.39181350.30662654X-RAY DIFFRACTION99
3.9062-4.92070.26391300.21642646X-RAY DIFFRACTION99
4.9207-48.97240.23051370.18852770X-RAY DIFFRACTION99

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