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- PDB-7pk5: Phosphodiesterase PdeL (EAL domain of crystals comprising full-le... -

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Basic information

Entry
Database: PDB / ID: 7pk5
TitlePhosphodiesterase PdeL (EAL domain of crystals comprising full-length protein)
ComponentsCyclic di-GMP phosphodiesterase PdeL
KeywordsHYDROLASE / c-di-GMP / phosphodiesterase / DNA binding
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / regulation of single-species biofilm formation / cyclic-guanylate-specific phosphodiesterase activity / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / protein homodimerization activity / metal ion binding / plasma membrane
Similarity search - Function
: / 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 ...: / 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
Similarity search - Domain/homology
Cyclic di-GMP phosphodiesterase PdeL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.4 Å
AuthorsFadel, J. / Schirmer, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Phosphodiesterase PdeL (EAL domain of crystals comprising full-length protein)
Authors: Schirmer, T. / Fadel, F.
History
DepositionAug 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic di-GMP phosphodiesterase PdeL
D: Cyclic di-GMP phosphodiesterase PdeL
B: Cyclic di-GMP phosphodiesterase PdeL
C: Cyclic di-GMP phosphodiesterase PdeL


Theoretical massNumber of molelcules
Total (without water)166,6794
Polymers166,6794
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-42 kcal/mol
Surface area42020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.408, 170.209, 93.085
Angle α, β, γ (deg.)90.000, 94.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cyclic di-GMP phosphodiesterase PdeL


Mass: 41669.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pdeL, yahA, b0315, JW0307 / Production host: Escherichia coli (E. coli)
References: UniProt: P21514, 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: 4.19 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.3 M Sodium acetate trihydrate 0.1 M Tris 7.5 8 % w/v PEG 20,000 8 % v/v PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 4.4→48.41 Å / Num. obs: 16934 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.053 / Rrim(I) all: 0.142 / Net I/σ(I): 7.8 / Num. measured all: 120886 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4.4-4.927.30.8073520148010.8850.3180.8682.299.8
9.84-48.417.10.0461111115670.9990.0190.0532.799

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.4 Å48.41 Å
Translation4.4 Å48.41 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lyk

4lyk


Resolution: 4.4→25 Å / Cor.coef. Fo:Fc: 0.829 / Cor.coef. Fo:Fc free: 0.703 / SU B: 0.023 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.184 / ESU R Free: 1.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3972 838 5 %RANDOM
Rwork0.3731 ---
obs0.3743 15989 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 186.58 Å2 / Biso mean: 112.145 Å2 / Biso min: 73.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å26.34 Å2
2---21.94 Å2-0 Å2
3---20.5 Å2
Refinement stepCycle: final / Resolution: 4.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7888 0 0 0 7888
Num. residues----1012
LS refinement shellResolution: 4.4→4.511 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 82 -
Rwork0.395 1119 -
all-1201 -
obs--99.26 %

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