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- PDB-7k5n: Ligand binding domain (tandem PAS/dCache) of Aeromonas caviae dig... -

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Basic information

Entry
Database: PDB / ID: 7k5n
TitleLigand binding domain (tandem PAS/dCache) of Aeromonas caviae diguanylate cyclase with proline bound
ComponentsSensor domain-containing diguanylate cyclase
KeywordsSIGNALING PROTEIN / PAS / Cache / bacterial inner membrane bound / amino acid binder
Function / homology
Function and homology information


membrane => GO:0016020 / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
PROLINE / Diguanylate cyclase
Similarity search - Component
Biological speciesAeromonas caviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSweeney, E.G. / Remington, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM125576 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01HD22486 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)5F32DK108591-03 United States
CitationJournal: Cell Host Microbe / Year: 2021
Title: Host-emitted amino acid cues regulate bacterial chemokinesis to enhance colonization.
Authors: Robinson, C.D. / Sweeney, E.G. / Ngo, J. / Ma, E. / Perkins, A. / Smith, T.J. / Fernandez, N.L. / Waters, C.M. / Remington, S.J. / Bohannan, B.J.M. / Guillemin, K.
History
DepositionSep 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor domain-containing diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6643
Polymers31,4571
Non-polymers2072
Water54030
1
A: Sensor domain-containing diguanylate cyclase
hetero molecules

A: Sensor domain-containing diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3286
Polymers62,9132
Non-polymers4144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+1,y,-z+11
Buried area2800 Å2
ΔGint-12 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.188, 86.188, 75.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Sensor domain-containing diguanylate cyclase


Mass: 31456.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: zebrafish isolate Guillemin lab, ZOR0002 / Source: (gene. exp.) Aeromonas caviae (bacteria) / Gene: C0708_15830, C1C92_04435 / Plasmid: pBH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3S5WQC2
#2: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: crystal growth conditions: 80 mM sodium acetate trihydrate pH 4.5 and 1.4 - 1.5 M sodium formate. cryoprotectant was the crystal growth conditions plus 10 mM proline and 20% glycerol. ...Details: crystal growth conditions: 80 mM sodium acetate trihydrate pH 4.5 and 1.4 - 1.5 M sodium formate. cryoprotectant was the crystal growth conditions plus 10 mM proline and 20% glycerol. crystals were briefly (< 1min) swished through cryoprotectant before flash frozen in liquid nitrogen
Temp details: room temperature

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: collected under cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26946 / % possible obs: 99.99 % / Redundancy: 20 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.064 / Rrim(I) all: 0.089 / Net I/σ(I): 30
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1304 / CC1/2: 0.208 / CC star: 0.586

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c8c

3c8c


Resolution: 1.8→30.47 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 39.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2607 1332 5 %
Rwork0.2362 25331 -
obs0.2375 26663 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.91 Å2 / Biso mean: 62.9754 Å2 / Biso min: 35.5 Å2
Refinement stepCycle: final / Resolution: 1.8→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 26 30 1945
Biso mean--55.17 54.49 -
Num. residues----237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.54471230.49542359248294
1.86-1.940.49491300.47512432256297
1.94-2.020.34631310.33212485261699
2.02-2.130.36381320.308725222654100
2.13-2.260.38891340.301625292663100
2.26-2.440.29051340.255825392673100
2.44-2.680.32271320.26225472679100
2.68-3.070.29081350.259525582693100
3.07-3.870.24761380.222326062744100
3.87-30.470.21221430.200227542897100

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