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- PDB-6ttr: Crystal Structure of the coiled coil and GGDEF domain of DgcB fro... -

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Basic information

Entry
Database: PDB / ID: 6ttr
TitleCrystal Structure of the coiled coil and GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP
ComponentsGGDEF diguanylate cyclase DgcB
KeywordsSIGNALING PROTEIN / GGDEF / c-di-GMP / cyclic di-GMP / Caulobacter / DgcB / diguanylate cyclase / DGC
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / nucleotide binding / plasma membrane
Similarity search - Function
: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Chem-C2E / PHOSPHATE ION / diguanylate cyclase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHolzschuh, F. / Schirmer, T. / Teixeira, R.D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-166652 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of the coiled coil and GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP
Authors: Holzschuh, F. / Schirmer, T. / Teixeira, R.D.
History
DepositionDec 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: GGDEF diguanylate cyclase DgcB
B: GGDEF diguanylate cyclase DgcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2637
Polymers48,0012
Non-polymers2,2615
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-15 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.084, 148.745, 60.401
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein GGDEF diguanylate cyclase DgcB


Mass: 24000.729 Da / Num. of mol.: 2 / Mutation: E261A, E262A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain NA1000 / CB15N) (bacteria)
Gene: dgcB, CCNA_01926 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3CAN8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: 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


Mass: 690.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H24N10O14P2
Has ligand of interestN

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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: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.09 M Sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09 M Ammonium sulfate, 0.1 M Tris BICINE, 20% v/v Glycerol, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→47.24 Å / Num. obs: 17722 / % possible obs: 94.2 % / Redundancy: 2.5 % / Biso Wilson estimate: 62.24 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.099 / Rrim(I) all: 0.14 / Χ2: 0.92 / Net I/σ(I): 6.5
Reflection shellResolution: 2.85→3.01 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2616 / CC1/2: 0.53 / Rpim(I) all: 0.708 / Rrim(I) all: 1.008 / Χ2: 0.98 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDS20180808data reduction
Aimless0.6.2data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DgcB GGDEF

Resolution: 2.85→47.24 Å / SU ML: 0.4265 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9431 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2656 883 4.99 %
Rwork0.2168 16826 -
obs0.2192 17709 92.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.31 Å2
Refinement stepCycle: LAST / Resolution: 2.85→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 148 0 3092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563147
X-RAY DIFFRACTIONf_angle_d1.0224280
X-RAY DIFFRACTIONf_chiral_restr0.0518473
X-RAY DIFFRACTIONf_plane_restr0.0039547
X-RAY DIFFRACTIONf_dihedral_angle_d21.05471880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.030.35181450.32592852X-RAY DIFFRACTION95.75
3.03-3.270.36221330.28362884X-RAY DIFFRACTION96.67
3.27-3.60.29421460.24232758X-RAY DIFFRACTION92.93
3.6-4.120.28641330.21992797X-RAY DIFFRACTION91.99
4.12-5.190.23081630.17472804X-RAY DIFFRACTION93.01
5.19-47.240.22551630.18922731X-RAY DIFFRACTION86.23

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