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- PDB-3pjt: Structure of Pseudomonas fluorescence LapD EAL domain complexed w... -

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Basic information

Entry
Database: PDB / ID: 3pjt
TitleStructure of Pseudomonas fluorescence LapD EAL domain complexed with c-di-GMP, C2221
ComponentsCyclic dimeric GMP binding protein
KeywordsLYASE / Tim Barrel / c-di-GMP receptor
Function / homology
Function and homology information


nucleotide binding / signal transduction / membrane / identical protein binding
Similarity search - Function
LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain ...LapD/MoxY periplasmic domain, C-terminal / LapD/MoxY, periplasmic domain / LapD/MoxY periplasmic domain / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / Diguanylate cyclase/phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5154 Å
AuthorsSondermann, H. / Navarro, M.V.A.S. / Krasteva, P.
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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Cyclic dimeric GMP binding protein
B: Cyclic dimeric GMP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9674
Polymers56,5872
Non-polymers1,3812
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-3 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.445, 204.830, 142.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cyclic dimeric GMP binding protein


Mass: 28293.305 Da / Num. of mol.: 2 / Fragment: UNP Residues 400-648
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
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, 0.2 M Ammonium sulfate, 24% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 21133 / Num. obs: 20943 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.59 Å / % possible all: 94.4

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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: 2.5154→34.138 Å / SU ML: 0.37 / σ(F): 0.2 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1923 9.55 %RANDOM
Rwork0.1808 ---
obs0.187 20130 94.82 %-
all-21133 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.309 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.1153 Å2-0 Å20 Å2
2---5.4216 Å20 Å2
3---10.5369 Å2
Refinement stepCycle: LAST / Resolution: 2.5154→34.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 92 115 4073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094044
X-RAY DIFFRACTIONf_angle_d1.2715484
X-RAY DIFFRACTIONf_dihedral_angle_d24.6421602
X-RAY DIFFRACTIONf_chiral_restr0.082600
X-RAY DIFFRACTIONf_plane_restr0.005702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5154-2.57830.33151110.22611045X-RAY DIFFRACTION77
2.5783-2.6480.31511200.21361165X-RAY DIFFRACTION87
2.648-2.72590.29391300.21111235X-RAY DIFFRACTION91
2.7259-2.81380.29731330.20671249X-RAY DIFFRACTION93
2.8138-2.91440.29171340.20391297X-RAY DIFFRACTION95
2.9144-3.0310.31411360.22431273X-RAY DIFFRACTION95
3.031-3.16880.30971410.21421330X-RAY DIFFRACTION97
3.1688-3.33580.28521390.20161303X-RAY DIFFRACTION98
3.3358-3.54460.24371430.18011357X-RAY DIFFRACTION99
3.5446-3.81790.21711440.16651349X-RAY DIFFRACTION99
3.8179-4.20150.19161430.14251372X-RAY DIFFRACTION99
4.2015-4.8080.18731450.13191364X-RAY DIFFRACTION99
4.808-6.05210.21831470.15031402X-RAY DIFFRACTION99
6.0521-34.14150.18361570.16631466X-RAY DIFFRACTION99

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