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- PDB-3hv9: Crystal structure of FimX EAL domain from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3hv9
TitleCrystal structure of FimX EAL domain from Pseudomonas aeruginosa
ComponentsProtein FimX
KeywordsHYDROLASE / EAL phosphodiesterase / biofilm / c-di-GMP
Function / homology
Function and homology information


regulation of single-species biofilm formation / cyclic-guanylate-specific phosphodiesterase activity / cell envelope / phosphorelay signal transduction system / nucleotide binding / regulation of DNA-templated transcription / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. ...EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / 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
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsNavarro, M.V.A.S. / De, N. / Bae, N. / Sondermann, H.
CitationJournal: Structure / Year: 2009
Title: Structural analysis of the GGDEF-EAL domain-containing c-di-GMP receptor FimX.
Authors: Navarro, M.V. / De, N. / Bae, N. / Wang, Q. / Sondermann, H.
History
DepositionJun 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FimX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6157
Polymers29,0621
Non-polymers5536
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.900, 107.900, 131.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Protein FimX


Mass: 29061.959 Da / Num. of mol.: 1 / Fragment: EAL domain: UNP residues 429-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fimX, PA4959 / Plasmid: ppSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9HUK6, cyclic-guanylate-specific phosphodiesterase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: Ammonium sulfate, PEG 8000, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2008
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.298→46.732 Å / Num. all: 20760 / Num. obs: 20719 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 31.7
Reflection shellResolution: 2.298→2.43 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6702 / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HVB

3hvb
PDB Unreleased entry


Resolution: 2.298→46.722 Å / SU ML: 0.3 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1034 4.99 %RANDOM
Rwork0.1952 ---
all0.2015 20719 --
obs0.1973 20712 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.751 Å2 / ksol: 0.369 e/Å3
Refinement stepCycle: LAST / Resolution: 2.298→46.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 36 117 2177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.298-2.41910.31011430.23362720X-RAY DIFFRACTION99
2.4191-2.57060.30861450.232772X-RAY DIFFRACTION100
2.5706-2.76910.27691440.22082745X-RAY DIFFRACTION100
2.7691-3.04770.27771470.2082784X-RAY DIFFRACTION100
3.0477-3.48860.29541470.20152802X-RAY DIFFRACTION100
3.4886-4.39470.19551500.16522843X-RAY DIFFRACTION100
4.3947-46.7320.18471580.18423012X-RAY DIFFRACTION99

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