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- PDB-4zvd: Crystal structure of MID domain of the E. coli DosC - form II -

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Basic information

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


diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / 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 ...diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / 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 / Globin/Protoglobin / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Diguanylate cyclase DosC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)29,3572
Polymers29,3572
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-13 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.930, 51.260, 92.650
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: 14678.621 Da / Num. of mol.: 2 / Fragment: UNP residues 173-298
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.: 62 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2M ammonium dihydrogen phosphate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 16326 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 25.22
Reflection shellResolution: 1.9→2 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 4.48 / % possible all: 100

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Processing

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

4zvc


Resolution: 1.9→46.325 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 817 5 %
Rwork0.2368 --
obs0.2391 16326 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 0 62 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041900
X-RAY DIFFRACTIONf_angle_d0.7232561
X-RAY DIFFRACTIONf_dihedral_angle_d12.069711
X-RAY DIFFRACTIONf_chiral_restr0.029287
X-RAY DIFFRACTIONf_plane_restr0.003329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.01910.37031320.27362509X-RAY DIFFRACTION100
2.0191-2.1750.32241340.23692541X-RAY DIFFRACTION100
2.175-2.39390.30771340.23062548X-RAY DIFFRACTION100
2.3939-2.74030.26561360.23882584X-RAY DIFFRACTION100
2.7403-3.45230.30271370.252606X-RAY DIFFRACTION100
3.4523-46.33880.25381440.22642721X-RAY DIFFRACTION100

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