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- PDB-4zve: Crystal structure of GGDEF domain of the E. coli DosC - form I (a... -

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Basic information

Entry
Database: PDB / ID: 4zve
TitleCrystal structure of GGDEF domain of the E. coli DosC - form I (apo-form)
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 / oxygen binding / heme binding / GTP binding / protein homodimerization activity ...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 / oxygen binding / heme binding / GTP binding / protein homodimerization activity / metal ion binding / plasma membrane
Similarity search - Function
: / DosC CZB-like middle domain / Diguanylate cyclase DosC, globin sensor domain / Globin-sensor domain / Protoglobin / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase ...: / DosC CZB-like middle domain / Diguanylate cyclase DosC, globin sensor domain / Globin-sensor domain / Protoglobin / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Globin/Protoglobin / Reverse transcriptase/Diguanylate cyclase domain / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Diguanylate cyclase DosC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2174
Polymers19,9011
Non-polymers3163
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint5 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.830, 70.830, 34.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 19900.594 Da / Num. of mol.: 1 / 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: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M tri-sodium citrate pH 5.6, 0.2 M ammonium acetate, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91162 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91162 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 54503 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.99
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 6.28 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IGN

3ign


Resolution: 1.2→35.415 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 10.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1455 2726 5 %
Rwork0.1231 --
obs0.1242 54503 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→35.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 21 185 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081463
X-RAY DIFFRACTIONf_angle_d1.2372007
X-RAY DIFFRACTIONf_dihedral_angle_d13.772581
X-RAY DIFFRACTIONf_chiral_restr0.081230
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22190.15341420.12712682X-RAY DIFFRACTION99
1.2219-1.24540.10331430.10852718X-RAY DIFFRACTION100
1.2454-1.27080.14091410.10012679X-RAY DIFFRACTION100
1.2708-1.29840.12211420.09862712X-RAY DIFFRACTION100
1.2984-1.32860.10951430.09082718X-RAY DIFFRACTION100
1.3286-1.36190.10961440.08742727X-RAY DIFFRACTION100
1.3619-1.39870.10671420.08442705X-RAY DIFFRACTION100
1.3987-1.43980.11731420.08792700X-RAY DIFFRACTION100
1.4398-1.48630.10461430.08752710X-RAY DIFFRACTION100
1.4863-1.53940.10461430.08322709X-RAY DIFFRACTION100
1.5394-1.60110.11321430.0882726X-RAY DIFFRACTION100
1.6011-1.67390.13081430.0962705X-RAY DIFFRACTION100
1.6739-1.76220.11851440.10372744X-RAY DIFFRACTION100
1.7622-1.87260.1321430.11132714X-RAY DIFFRACTION100
1.8726-2.01720.14721440.1142731X-RAY DIFFRACTION100
2.0172-2.22010.14081440.11452749X-RAY DIFFRACTION100
2.2201-2.54130.15841450.1352749X-RAY DIFFRACTION100
2.5413-3.20150.15451450.14942765X-RAY DIFFRACTION100
3.2015-35.43040.17941500.1482834X-RAY DIFFRACTION100

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