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- PDB-4kie: Crystal structure of the EAL domain of c-di-GMP specific phosphod... -

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Basic information

Entry
Database: PDB / ID: 4kie
TitleCrystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA
ComponentsCyclic di-GMP phosphodiesterase YahA
KeywordsHYDROLASE / pGpG / phosphodiesterase / TIM-barrel
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / cyclic-guanylate-specific phosphodiesterase activity / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / protein homodimerization activity / metal ion binding
Similarity search - Function
EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family ...EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Cyclic di-GMP phosphodiesterase PdeL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSundriyal, A. / Schirmer, T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Inherent Regulation of EAL Domain-catalyzed Hydrolysis of Second Messenger Cyclic di-GMP.
Authors: Sundriyal, A. / Massa, C. / Samoray, D. / Zehender, F. / Sharpe, T. / Jenal, U. / Schirmer, T.
History
DepositionMay 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references / Other
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic di-GMP phosphodiesterase YahA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9936
Polymers31,2421
Non-polymers7515
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.626, 87.818, 94.723
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Cyclic di-GMP phosphodiesterase YahA


Mass: 31241.881 Da / Num. of mol.: 1 / Fragment: EAL domain containing residues 96-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yahA, b0315, JW0307 / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: P21514, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Na-Acetate pH 4.6 and 40% PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.36 Å / Num. obs: 34026 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.14 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.722
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.7-1.796.140.441.66301084904100
1.79-1.96.160.272.74287324663100
1.9-2.036.180.164.28270154374100
2.03-2.196.190.116.65254434111100
2.19-2.46.190.079.19234063783100
2.4-2.696.210.0610.12212303417100
2.69-3.16.190.078.9188203042100
3.1-3.86.160.0415.1159932598100
3.8-5.386.030.0316.0712248203099.74
5.38-47.365.510.0320.636088110494.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
SCALACCP4_3.3.20data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R6O

2r6o


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 3.381 / SU ML: 0.057 / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflection
Rfree0.1853 1726 5.1 %
Rwork0.1654 --
obs0.1665 34019 99.73 %
Solvent computationSolvent model: MASK
Displacement parametersBiso max: 72.27 Å2 / Biso mean: 27.497 Å2 / Biso min: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0 Å2
2---0.71 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 50 213 2317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192214
X-RAY DIFFRACTIONr_bond_other_d0.0010.022124
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9683005
X-RAY DIFFRACTIONr_angle_other_deg0.79534910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24325.05199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67715354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.512156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02492
LS refinement shellResolution: 1.7→1.744 Å
RfactorNum. reflection% reflection
Rfree0.282 116 -
Rwork0.234 2340 -
all-2456 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: -0.2854 Å / Origin y: -18.2126 Å / Origin z: -24.3855 Å
111213212223313233
T0.0019 Å20.0002 Å20.0063 Å2-0.0075 Å20.0096 Å2--0.0543 Å2
L0.4432 °2-0.1825 °20.054 °2-0.4183 °2-0.0164 °2--0.2172 °2
S-0.0193 Å °-0.0152 Å °-0.1081 Å °0.0105 Å °0.0318 Å °0.0058 Å °0.0116 Å °-0.0205 Å °-0.0125 Å °

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