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- PDB-4zva: Crystal structure of globin domain of the E. coli DosC - form I (... -

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Basic information

Entry
Database: PDB / ID: 4zva
TitleCrystal structure of globin domain of the E. coli DosC - form I (ferric)
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 / SAD / Resolution: 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 1.1May 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,0404
Polymers37,8072
Non-polymers1,2332
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-52 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.410, 97.410, 152.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-363-

HOH

21B-362-

HOH

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Components

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


Mass: 18903.477 Da / Num. of mol.: 2 / Fragment: UNP residues 8-170
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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M tri-sodium citrate pH 5.6, 0.2 M ammonium acetate, 27% (w/v) PEG 4000

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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→50 Å / Num. obs: 29494 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.44
Reflection shellResolution: 2→2.1 Å / Redundancy: 11 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 3.52 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→48.705 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 1475 5 %
Rwork0.2221 --
obs0.2238 29493 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 86 137 2619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032546
X-RAY DIFFRACTIONf_angle_d0.8563476
X-RAY DIFFRACTIONf_dihedral_angle_d12.366922
X-RAY DIFFRACTIONf_chiral_restr0.023378
X-RAY DIFFRACTIONf_plane_restr0.003436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06460.32251310.28532492X-RAY DIFFRACTION100
2.0646-2.13840.35641300.28062470X-RAY DIFFRACTION100
2.1384-2.2240.3391320.26512514X-RAY DIFFRACTION100
2.224-2.32520.28291310.27112489X-RAY DIFFRACTION100
2.3252-2.44780.26651330.26892516X-RAY DIFFRACTION100
2.4478-2.60120.29591320.27772506X-RAY DIFFRACTION100
2.6012-2.8020.32951330.25752534X-RAY DIFFRACTION100
2.802-3.08390.25311340.25812535X-RAY DIFFRACTION100
3.0839-3.530.25891350.22782576X-RAY DIFFRACTION100
3.53-4.4470.24041380.19092614X-RAY DIFFRACTION100
4.447-48.71940.21441460.17792772X-RAY DIFFRACTION100

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