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- PDB-4zvb: Crystal structure of globin domain of the E. coli DosC - form II ... -

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Basic information

Entry
Database: PDB / ID: 4zvb
TitleCrystal structure of globin domain of the E. coli DosC - form II (ferrous)
ComponentsDiguanylate cyclase DosC
KeywordsSIGNALING PROTEIN / oxygen sensing / diguanylate cyclase / cyclic-di-GMP / transferase
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 / Globins / Globin-like / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Diguanylate cyclase DosC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

Downloads & links

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Assembly

Deposited unit
A: Diguanylate cyclase DosC
B: Diguanylate cyclase DosC
C: Diguanylate cyclase DosC
D: Diguanylate cyclase DosC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9268
Polymers76,4604
Non-polymers2,4664
Water1,22568
1
A: Diguanylate cyclase DosC
B: Diguanylate cyclase DosC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4634
Polymers38,2302
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-47 kcal/mol
Surface area13750 Å2
MethodPISA
2
C: Diguanylate cyclase DosC
D: Diguanylate cyclase DosC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4634
Polymers38,2302
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-50 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.960, 58.270, 59.400
Angle α, β, γ (deg.)79.52, 75.69, 75.29
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 19115.004 Da / Num. of mol.: 4 / Fragment: UNP residues 1-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: dosC, yddV, b1490, JW5241 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA89, diguanylate cyclase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium phosphate-citrate pH 4.2, 0.2 M sodium chloride, 16% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.7345 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7345 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22142 / % possible obs: 94.6 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.36
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.64 / % possible all: 88.3

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Processing

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

4zva


Resolution: 2.4→45.341 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 1107 5 %
Rwork0.2173 --
obs0.219 22138 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 172 68 5098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025160
X-RAY DIFFRACTIONf_angle_d0.6987036
X-RAY DIFFRACTIONf_dihedral_angle_d10.8731886
X-RAY DIFFRACTIONf_chiral_restr0.019762
X-RAY DIFFRACTIONf_plane_restr0.003880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50930.37311300.3092451X-RAY DIFFRACTION88
2.5093-2.64150.31481340.2542551X-RAY DIFFRACTION92
2.6415-2.8070.28591380.23552617X-RAY DIFFRACTION94
2.807-3.02370.24751390.21562650X-RAY DIFFRACTION95
3.0237-3.32790.25421390.22572647X-RAY DIFFRACTION96
3.3279-3.80930.26221410.21092673X-RAY DIFFRACTION96
3.8093-4.79840.2141430.19282718X-RAY DIFFRACTION97
4.7984-45.34950.22441430.20842724X-RAY DIFFRACTION98

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