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- PDB-6tts: Crystal structure of the GGDEF domain of DgcB from Caulobacter cr... -

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Basic information

Entry
Database: PDB / ID: 6tts
TitleCrystal structure of the 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 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / diguanylate cyclase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHolzschuh, F. / Schirmer, T. / Teixeira, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-166652 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of the GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP
Authors: Holzschuh, F. / Schirmer, T. / Teixeira, R.
History
DepositionDec 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)46,92813
Polymers42,9002
Non-polymers4,02811
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-52 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.500, 64.500, 246.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

#1: Protein GGDEF diguanylate cyclase DgcB


Mass: 21449.895 Da / Num. of mol.: 2
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-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.: 5 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M LiSO4, 0.1 M NaAcet pH 5.5, 8% w/v PEG 20k, 8% v/v PEG 500 MME, 500 uM c-di-GMP, 1 mM GTP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97947 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.5→64.5 Å / Num. obs: 19045 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 29.29 Å2 / CC1/2: 0.813 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.088 / Rrim(I) all: 0.183 / Χ2: 0.95 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2068 / CC1/2: 0.693 / Rpim(I) all: 0.427 / Rrim(I) all: 0.672 / Χ2: 0.89 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLM7.2.2data reduction
Aimless0.6.2data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ign, 3hva, 3qyy, 3i5c, 4wxw, 3tvk, 4urg, 4zvf, 4h54, 4zmm, 3icl, 4iob, 5euh, 3ezu, 4yme

3ign

3hva

3qyy

3i5c

4wxw

3tvk

4urg

4zvf

4h54

4zmm

3icl

4iob

5euh

3ezu

4yme


Resolution: 2.5→50.76 Å / SU ML: 0.3133 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2429 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2608 1002 5.28 %
Rwork0.2035 17972 -
obs0.2065 18974 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.68 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 260 16 2921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982967
X-RAY DIFFRACTIONf_angle_d1.35884061
X-RAY DIFFRACTIONf_chiral_restr0.0664438
X-RAY DIFFRACTIONf_plane_restr0.0063496
X-RAY DIFFRACTIONf_dihedral_angle_d26.92721101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.34181480.26532454X-RAY DIFFRACTION98.9
2.63-2.80.30091290.25232520X-RAY DIFFRACTION99.92
2.8-3.010.33381360.24642520X-RAY DIFFRACTION99.96
3.01-3.320.32061460.232525X-RAY DIFFRACTION99.96
3.32-3.80.22371420.19062586X-RAY DIFFRACTION100
3.8-4.780.22911440.16532586X-RAY DIFFRACTION100
4.78-50.760.21191570.17812781X-RAY DIFFRACTION99.83

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