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- PDB-3hva: Crystal structure of FimX GGDEF domain from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3hva
TitleCrystal structure of FimX GGDEF domain from Pseudomonas aeruginosa
ComponentsProtein FimX
KeywordsTRANSFERASE / GGDEF diguanylate cyclase / 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
: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF 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 / Reverse transcriptase/Diguanylate cyclase domain / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.042 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FimX
B: Protein FimX


Theoretical massNumber of molelcules
Total (without water)38,2652
Polymers38,2652
Non-polymers00
Water2,576143
1
A: Protein FimX


Theoretical massNumber of molelcules
Total (without water)19,1331
Polymers19,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein FimX


Theoretical massNumber of molelcules
Total (without water)19,1331
Polymers19,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.179, 94.111, 45.504
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein FimX


Mass: 19132.561 Da / Num. of mol.: 2 / Fragment: GGDEF domain: UNP residues 260-431
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, diguanylate cyclase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.9 Å3/Da / Density % sol: 35.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 2, 2007
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.191
ReflectionResolution: 2→47 Å / Num. all: 18605 / Num. obs: 17415 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.7
Reflection shellResolution: 2→2.09 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2270 / % possible all: 76.1

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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 1W25

1w25


Resolution: 2.042→27.118 Å / σ(F): 0.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 881 5.27 %RANDOM
Rwork0.2126 ---
all0.2203 17415 --
obs0.2143 16711 94.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.249 Å2 / ksol: 0.388 e/Å3
Refinement stepCycle: LAST / Resolution: 2.042→27.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 0 143 2599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.042-2.13480.28361010.27051660X-RAY DIFFRACTION98
2.1348-2.24730.29081130.25761925X-RAY DIFFRACTION98
2.2473-2.3880.29711060.26461982X-RAY DIFFRACTION98
2.388-2.57230.24621130.25831972X-RAY DIFFRACTION98
2.5723-2.83090.2826900.24152055X-RAY DIFFRACTION98
2.8309-3.23990.2914980.22522071X-RAY DIFFRACTION98
3.2399-4.07970.2041220.16912078X-RAY DIFFRACTION98
4.0797-27.1180.21141080.1752117X-RAY DIFFRACTION98

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