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- PDB-6eib: Structure of the active GGEEF domain of a diguanylate cyclase fro... -

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Basic information

Entry
Database: PDB / ID: 6eib
TitleStructure of the active GGEEF domain of a diguanylate cyclase from Vibrio cholerae.
ComponentsSensory box/GGDEF family protein
KeywordsTRANSFERASE / diguanylate cyclase / GGEEF domain
Function / homology
Function and homology information


diguanylate cyclase / diguanylate cyclase activity / GTP binding / metal ion binding
Similarity search - Function
PAS fold-4 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain ...PAS fold-4 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Diguanylate cyclase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsChouhan, O.P. / Roske, Y.
Funding support Germany, 1items
OrganizationGrant numberCountry
DAAD91608443 Germany
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structure of the active GGEEF domain of a diguanylate cyclase from Vibrio cholerae.
Authors: Chouhan, O.P. / Roske, Y. / Heinemann, U. / Biswas, S.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Structure summary / Category: citation / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Sensory box/GGDEF family protein
B: Sensory box/GGDEF family protein
C: Sensory box/GGDEF family protein
D: Sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,07847
Polymers75,8064
Non-polymers3,27243
Water9,386521
1
A: Sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,82913
Polymers18,9511
Non-polymers87812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,95914
Polymers18,9511
Non-polymers1,00813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,86613
Polymers18,9511
Non-polymers91512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sensory box/GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4237
Polymers18,9511
Non-polymers4716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.905, 80.267, 71.696
Angle α, β, γ (deg.)90.00, 97.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sensory box/GGDEF family protein


Mass: 18951.459 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Gene: VC0395_0300 / Plasmid: pGEX_6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0H3AFM6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.2 / Details: 0.5M Ammonium sulfate, 0.1M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98141 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98141 Å / Relative weight: 1
ReflectionResolution: 1.94→43.41 Å / Num. obs: 52783 / % possible obs: 96.3 % / Redundancy: 2.34 % / Biso Wilson estimate: 32.69 Å2 / CC1/2: 0.995 / Rsym value: 0.094 / Net I/σ(I): 7.82
Reflection shellResolution: 1.94→2.06 Å / Mean I/σ(I) obs: 1.26 / Num. unique obs: 8471 / CC1/2: 0.687 / Rsym value: 0.763 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZVE

4zve


Resolution: 1.941→35.534 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.01
RfactorNum. reflection% reflection
Rfree0.2425 2100 3.98 %
Rwork0.1939 --
obs0.1958 52745 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.941→35.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 190 521 5905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115524
X-RAY DIFFRACTIONf_angle_d1.2477395
X-RAY DIFFRACTIONf_dihedral_angle_d14.1142022
X-RAY DIFFRACTIONf_chiral_restr0.061748
X-RAY DIFFRACTIONf_plane_restr0.007966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.941-1.98610.35871380.32333338X-RAY DIFFRACTION95
1.9861-2.03580.36151390.2963345X-RAY DIFFRACTION96
2.0358-2.09080.32931380.27233330X-RAY DIFFRACTION96
2.0908-2.15230.32471390.25863340X-RAY DIFFRACTION96
2.1523-2.22180.28581390.24163351X-RAY DIFFRACTION95
2.2218-2.30120.2731410.22363416X-RAY DIFFRACTION97
2.3012-2.39330.28641400.21923369X-RAY DIFFRACTION97
2.3933-2.50220.29591410.20883402X-RAY DIFFRACTION98
2.5022-2.63410.24871430.19423442X-RAY DIFFRACTION97
2.6341-2.7990.22611390.19153369X-RAY DIFFRACTION97
2.799-3.01510.22161390.18073356X-RAY DIFFRACTION96
3.0151-3.31830.23711380.16493326X-RAY DIFFRACTION95
3.3183-3.7980.19251420.15333415X-RAY DIFFRACTION97
3.798-4.78320.19291410.14853419X-RAY DIFFRACTION96
4.7832-35.53950.23211430.20243427X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.74130.07971.34821.22020.25623.5791-0.04670.09340.2462-0.1451-0.01860.0367-0.19890.04340.04180.19750.00150.00440.16230.01920.224816.965138.5451-9.9356
23.0349-0.52381.1561.5077-0.47461.83470.14080.1347-0.3395-0.0511-0.09380.00980.26660.0844-0.04930.22970.0057-0.00830.1418-0.01110.185310.2041-3.1106-17.4055
31.1714-0.2517-0.35253.0350.43572.18920.04440.10240.0452-0.33550.04070.2595-0.0985-0.122-0.07820.27840.0039-0.07920.20680.01960.2164-2.602117.7207-25.1749
41.95241.30961.05264.58832.01511.76060.3186-0.2958-0.1380.8506-0.2705-0.1590.5143-0.2869-0.03720.4036-0.0666-0.05590.26310.03470.207421.249717.44944.8532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 159 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 161 )
3X-RAY DIFFRACTION3chain 'C' and (resid 3 through 159 )
4X-RAY DIFFRACTION4chain 'D' and (resid 4 through 159 )

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