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- PDB-4fok: 1.8 A Crystal structure of the FimX EAL domain in complex with c-diGMP -

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Basic information

Entry
Database: PDB / ID: 4fok
Title1.8 A Crystal structure of the FimX EAL domain in complex with c-diGMP
ComponentsFimX
KeywordsPROTEIN BINDING / TIM like Barrel / beta-(beta/alpha)6-beta / c-di-GMP binding / Type IV pilus assembly / PilZ
Function / homology
Function and homology information


nucleotide binding / metal ion binding
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. / GGDEF domain ...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 / CheY-like superfamily / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / PAS domain S-box protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFarah, C.S. / Guzzo, C.R.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structure of the PilZ-FimXEAL-c-di-GMP Complex Responsible for the Regulation of Bacterial Type IV Pilus Biogenesis.
Authors: Guzzo, C.R. / Dunger, G. / Salinas, R.K. / Farah, C.S.
History
DepositionJun 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: FimX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,04010
Polymers29,6121
Non-polymers1,4279
Water3,657203
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.676, 85.515, 46.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein FimX


Mass: 29612.451 Da / Num. of mol.: 1 / Fragment: EAL domain (UNP residues 426-689)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: XAC2398 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8PJX9
#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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 0.6 M amonium sulfate, 0.1 M sodium citrate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.437 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 30, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.437 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 24851 / Num. obs: 24851 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.125 / Net I/σ(I): 16.56
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.25 / Rsym value: 0.67 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.251 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19786 1258 5.1 %RANDOM
Rwork0.15487 ---
obs0.157 23469 99.41 %-
all-23469 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 94 203 2382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222428
X-RAY DIFFRACTIONr_bond_other_d0.0010.021686
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9963326
X-RAY DIFFRACTIONr_angle_other_deg0.93234102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5775313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2123.443122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75515410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5391524
X-RAY DIFFRACTIONr_chiral_restr0.090.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8291.51421
X-RAY DIFFRACTIONr_mcbond_other0.2471.5570
X-RAY DIFFRACTIONr_mcangle_it1.49222314
X-RAY DIFFRACTIONr_scbond_it2.4131007
X-RAY DIFFRACTIONr_scangle_it3.8084.5992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 84 -
Rwork0.192 1679 -
obs--98.82 %

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