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- PDB-4zvc: Crystal structure of MID domain of the E. coli DosC - form I -

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Basic information

Entry
Database: PDB / ID: 4zvc
TitleCrystal structure of MID domain of the E. coli DosC - form I
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 / Globin/Protoglobin / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
BENZOIC ACID / Diguanylate cyclase DosC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 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 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Diguanylate cyclase DosC
B: Diguanylate cyclase DosC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4793
Polymers29,3572
Non-polymers1221
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-8 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.220, 43.570, 52.440
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 1.88 Å3/Da / Density % sol: 34.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M Bis-Tris pH 5.5, 0.2M magnesium chloride, 17% (w/v) PEG 3350, 0.1M Gd-HPDO3A [gadolinium complex of 10-(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid]

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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: 1.5→50 Å / Num. obs: 35038 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.57
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.37 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→48.325 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 1752 5 %
Rwork0.1474 --
obs0.1495 35037 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→48.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 9 255 2167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071995
X-RAY DIFFRACTIONf_angle_d0.9782703
X-RAY DIFFRACTIONf_dihedral_angle_d12.822764
X-RAY DIFFRACTIONf_chiral_restr0.041303
X-RAY DIFFRACTIONf_plane_restr0.005350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54060.3321340.22182552X-RAY DIFFRACTION100
1.5406-1.58590.20811340.16312547X-RAY DIFFRACTION100
1.5859-1.63710.22671320.14482516X-RAY DIFFRACTION100
1.6371-1.69560.21161350.12882556X-RAY DIFFRACTION99
1.6956-1.76350.18551330.12372528X-RAY DIFFRACTION100
1.7635-1.84380.17871340.12012536X-RAY DIFFRACTION100
1.8438-1.9410.17711350.1242565X-RAY DIFFRACTION100
1.941-2.06260.18141340.12852565X-RAY DIFFRACTION100
2.0626-2.22180.17021350.13142551X-RAY DIFFRACTION100
2.2218-2.44540.18851350.13352573X-RAY DIFFRACTION100
2.4454-2.79920.21350.14852566X-RAY DIFFRACTION100
2.7992-3.52660.16821370.15842592X-RAY DIFFRACTION100
3.5266-48.35020.1861390.16762638X-RAY DIFFRACTION99

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