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- PDB-4zvg: Crystal structure of GGDEF domain of the E. coli DosC - form III -

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Basic information

Entry
Database: PDB / ID: 4zvg
TitleCrystal structure of GGDEF domain of the E. coli DosC - form III
ComponentsDiguanylate cyclase DosC
KeywordsSIGNALING PROTEIN / oxygen sensing / diguanylate cyclase / cyclic-di-GMP
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / carbon monoxide binding / response to oxygen levels / cell adhesion involved in single-species biofilm formation / response to stress / oxygen binding / heme binding / GTP binding ...negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / carbon monoxide binding / response to oxygen levels / cell adhesion involved in single-species biofilm formation / response to stress / oxygen binding / heme binding / GTP binding / protein homodimerization activity / metal ion binding / plasma membrane
Similarity search - Function
Diguanylate cyclase DosC, globin sensor domain / : / DosC CZB-like middle domain / Globin-sensor domain / Protoglobin / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain ...Diguanylate cyclase DosC, globin sensor domain / : / DosC CZB-like middle domain / Globin-sensor domain / Protoglobin / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Globin/Protoglobin / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Diguanylate cyclase DosC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTarnawski, M. / Barends, T.R.M. / Schlichting, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural analysis of an oxygen-regulated diguanylate cyclase.
Authors: Tarnawski, M. / Barends, T.R. / Schlichting, I.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: Diguanylate cyclase DosC
B: Diguanylate cyclase DosC


Theoretical massNumber of molelcules
Total (without water)39,8012
Polymers39,8012
Non-polymers00
Water1,40578
1
A: Diguanylate cyclase DosC


Theoretical massNumber of molelcules
Total (without water)19,9011
Polymers19,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diguanylate cyclase DosC


Theoretical massNumber of molelcules
Total (without water)19,9011
Polymers19,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.780, 58.930, 113.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diguanylate cyclase DosC / DGC / Direct oxygen-sensing cyclase


Mass: 19900.594 Da / Num. of mol.: 2 / Fragment: UNP residues 297-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dosC, yddV, b1490, JW5241 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA89, diguanylate cyclase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2M potassium sodium tartrate, 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97627 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18580 / % possible obs: 97.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.36
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.54 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZVE

4zve


Resolution: 2.2→48.61 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 929 5 %
Rwork0.2076 --
obs0.2098 18580 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 0 78 2738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082702
X-RAY DIFFRACTIONf_angle_d1.1323642
X-RAY DIFFRACTIONf_dihedral_angle_d11.7581022
X-RAY DIFFRACTIONf_chiral_restr0.047411
X-RAY DIFFRACTIONf_plane_restr0.006469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.31610.33721260.28852411X-RAY DIFFRACTION96
2.3161-2.46120.34231290.26892448X-RAY DIFFRACTION96
2.4612-2.65120.30241300.24692459X-RAY DIFFRACTION97
2.6512-2.91790.33191310.24022502X-RAY DIFFRACTION98
2.9179-3.34010.26481350.222557X-RAY DIFFRACTION99
3.3401-4.20780.23921350.18722575X-RAY DIFFRACTION99
4.2078-48.62150.19161430.17472699X-RAY DIFFRACTION99

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