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- PDB-4hu3: Crystal structure of EAL domain of the E. coli DosP - monomeric form -

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Basic information

Entry
Database: PDB / ID: 4hu3
TitleCrystal structure of EAL domain of the E. coli DosP - monomeric form
ComponentsOxygen sensor protein DosP
KeywordsSIGNALING PROTEIN / HYDROLASE / EAL domain / cyclic di-GMP phosphodiesterase / TIM-barrel / EcDos / direct oxygen sensor
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / cyclic-guanylate-specific phosphodiesterase activity / response to oxygen levels / oxygen sensor activity / heme binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Diguanylate cyclase/phosphodiesterase / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. ...Diguanylate cyclase/phosphodiesterase / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Nucleotide cyclase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Oxygen sensor protein DosP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.301 Å
AuthorsTarnawski, M. / Barends, T.R.M. / Hartmann, E. / Schlichting, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of the catalytic EAL domain of the Escherichia coli direct oxygen sensor.
Authors: Tarnawski, M. / Barends, T.R. / Hartmann, E. / Schlichting, I.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxygen sensor protein DosP


Theoretical massNumber of molelcules
Total (without water)32,8621
Polymers32,8621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.810, 139.810, 139.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Oxygen sensor protein DosP / / Direct oxygen-sensing phosphodiesterase / Direct oxygen sensor protein / Ec DOS / Heme-regulated ...Direct oxygen-sensing phosphodiesterase / Direct oxygen sensor protein / Ec DOS / Heme-regulated cyclic di-GMP phosphodiesterase /


Mass: 32861.820 Da / Num. of mol.: 1 / Fragment: EAL domain, UNP residues 529-799
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1489, dos, dosP, JW1484, yddU / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P76129, cyclic-guanylate-specific phosphodiesterase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.5 M potassium sodium tartrate, 0.1 M MES pH 6.3, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97139, 0.97896, 0.97139
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2007
RadiationMonochromator: Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971391
20.978961
ReflectionResolution: 3.3→40 Å / Num. obs: 13227 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 3.3→3.4 Å / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
RESOLVEphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 3.301→37.366 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.56 / σ(F): 1.37 / Phase error: 37.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3231 332 4.76 %RANDOM
Rwork0.2639 ---
all0.2667 ---
obs0.2667 6969 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.33 Å2 / Biso mean: 90.3734 Å2 / Biso min: 36.54 Å2
Refinement stepCycle: LAST / Resolution: 3.301→37.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 0 0 2125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022169
X-RAY DIFFRACTIONf_angle_d0.662939
X-RAY DIFFRACTIONf_chiral_restr0.048334
X-RAY DIFFRACTIONf_plane_restr0.003379
X-RAY DIFFRACTIONf_dihedral_angle_d12.256812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.301-4.15790.40551780.318132643442100
4.1579-37.36820.28821540.24293373352799

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