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- PDB-4ag0: Crystal structure of FimX EAL domain -

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Basic information

Entry
Database: PDB / ID: 4ag0
TitleCrystal structure of FimX EAL domain
ComponentsFIMX
KeywordsHYDROLASE / PHOSPHODIESTERASE / C-DIGMP / BIOFILM
Function / homology
Function and homology information


phosphorelay signal transduction system / nucleotide binding / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
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 ...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 / Nucleotide cyclase / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / PAS fold / PAS fold / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / FimX
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsRobert-Paganin, J. / Nonin-Lecomte, S. / Rety, S.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of an Eal Domain in Complex with Reaction Product 5'-Pgpg
Authors: Robert-Paganin, J. / Nonin-Lecomte, S. / Rety, S.
History
DepositionJan 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIMX
B: FIMX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9096
Polymers60,5652
Non-polymers3444
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-37.4 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.530, 87.660, 108.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FIMX


Mass: 30282.393 Da / Num. of mol.: 2 / Fragment: EAL DOMAIN, RESIDUES 439-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Gene: PA4959 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2
References: UniProt: Q9HUK6, cyclic-guanylate-specific phosphodiesterase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.49 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M NA ACETATE PH 4.5, 0.4 M K2HPO4, 1.2 M NAH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→46.05 Å / Num. obs: 27564 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.21
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.13 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R6O

2r6o


Resolution: 2.304→40.626 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2842 1357 4.9 %
Rwork0.2091 --
obs0.2127 27552 99.09 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.902 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 57.09 Å2
Baniso -1Baniso -2Baniso -3
1-15.1824 Å20 Å20 Å2
2---15.329 Å20 Å2
3---0.1465 Å2
Refinement stepCycle: LAST / Resolution: 2.304→40.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 19 115 4031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153994
X-RAY DIFFRACTIONf_angle_d1.5515425
X-RAY DIFFRACTIONf_dihedral_angle_d17.351453
X-RAY DIFFRACTIONf_chiral_restr0.076618
X-RAY DIFFRACTIONf_plane_restr0.008702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3041-2.38650.39731330.30072532X-RAY DIFFRACTION98
2.3865-2.4820.27861460.25642602X-RAY DIFFRACTION100
2.482-2.5950.36961220.25432602X-RAY DIFFRACTION100
2.595-2.73180.32361260.23762611X-RAY DIFFRACTION100
2.7318-2.90290.30391390.22032615X-RAY DIFFRACTION100
2.9029-3.12690.29261480.24072606X-RAY DIFFRACTION100
3.1269-3.44140.30191450.21182612X-RAY DIFFRACTION100
3.4414-3.93910.29421490.20832637X-RAY DIFFRACTION100
3.9391-4.96140.25391300.17432676X-RAY DIFFRACTION99
4.9614-40.6320.24151190.19232702X-RAY DIFFRACTION96

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