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- PDB-3hv8: Crystal structure of FimX EAL domain from Pseudomonas aeruginosa ... -

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Basic information

Entry
Database: PDB / ID: 3hv8
TitleCrystal structure of FimX EAL domain from Pseudomonas aeruginosa bound to c-di-GMP
ComponentsProtein FimX
KeywordsHYDROLASE / EAL phosphodiesterase / biofilm / c-di-GMP
Function / homology
Function and homology information


phosphorelay signal transduction system / nucleotide binding / regulation of DNA-templated transcription / identical protein binding / metal ion 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
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.445 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: 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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)30,0122
Polymers29,3211
Non-polymers6901
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.950, 93.950, 68.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein FimX


Mass: 29321.281 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-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
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 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 2, 2008
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.445→42.1 Å / Num. all: 54448 / Num. obs: 54441 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.6
Reflection shellResolution: 1.445→1.56 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.5 / Num. unique all: 8121 / % possible all: 92.3

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Processing

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

3hvb
PDB Unreleased entry


Resolution: 1.445→26.54 Å / SU ML: 0.89 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 2765 5.08 %RANDOM
Rwork0.1915 ---
all0.1956 55333 --
obs0.1925 54441 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.618 Å2 / ksol: 0.389 e/Å3
Refinement stepCycle: LAST / Resolution: 1.445→26.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 46 318 2253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.445-1.46960.31521190.29462067X-RAY DIFFRACTION80
1.4696-1.49630.2631310.25392475X-RAY DIFFRACTION96
1.4963-1.52510.28381460.25362562X-RAY DIFFRACTION99
1.5251-1.55620.2771240.24012585X-RAY DIFFRACTION99
1.5562-1.590.27121310.23052601X-RAY DIFFRACTION100
1.59-1.6270.25931580.23692519X-RAY DIFFRACTION100
1.627-1.66770.24241520.22062571X-RAY DIFFRACTION100
1.6677-1.71280.24451410.21352611X-RAY DIFFRACTION100
1.7128-1.76320.22541430.20882567X-RAY DIFFRACTION100
1.7632-1.82010.22251250.20212615X-RAY DIFFRACTION100
1.8201-1.88510.23111470.20352586X-RAY DIFFRACTION100
1.8851-1.96050.21021160.19582647X-RAY DIFFRACTION100
1.9605-2.04970.22031570.18992591X-RAY DIFFRACTION100
2.0497-2.15780.2141250.18652632X-RAY DIFFRACTION100
2.1578-2.29290.19471500.18352617X-RAY DIFFRACTION100
2.2929-2.46980.20471220.1892661X-RAY DIFFRACTION100
2.4698-2.71810.2311700.19572621X-RAY DIFFRACTION100
2.7181-3.11090.18671420.17972681X-RAY DIFFRACTION100
3.1109-3.91740.18861410.16092702X-RAY DIFFRACTION100
3.9174-26.540.17631250.17432765X-RAY DIFFRACTION96

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