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- PDB-4f48: The X-ray structural of FimXEAL-c-di-GMP-PilZ complexes from Xant... -

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Basic information

Entry
Database: PDB / ID: 4f48
TitleThe X-ray structural of FimXEAL-c-di-GMP-PilZ complexes from Xanthomonas campestris
Components
  • Putative uncharacterized protein
  • Type IV fimbriae assembly protein
KeywordsSIGNALING PROTEIN / FimXEAL-c-di-GMP-PilZ complex / type IV pilus
Function / homology
Function and homology information


cyclic-di-GMP binding / nucleotide binding
Similarity search - Function
predicted glycosyltransferase like domains / PilZ domain / PilZ domain / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain ...predicted glycosyltransferase like domains / PilZ domain / PilZ 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 / PAS domain / PAS domain superfamily / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / PAS domain S-box protein / Type IV fimbriae assembly protein
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsChin, K.-H. / Liao, Y.-T. / Chou, S.-H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural polymorphism of c-di-GMP bound to an EAL domain and in complex with a type II PilZ-domain protein.
Authors: Chin, K.-H. / Kuo, W.-T. / Yu, Y.-J. / Liao, Y.-T. / Yang, M.T. / Chou, S.-H.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 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: Putative uncharacterized protein
B: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1993
Polymers40,5082
Non-polymers6901
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein
B: Type IV fimbriae assembly protein
hetero molecules

A: Putative uncharacterized protein
B: Type IV fimbriae assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3976
Polymers81,0164
Non-polymers1,3812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9220 Å2
ΔGint-24 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.222, 158.222, 64.808
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

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Components

#1: Protein Putative uncharacterized protein / FimXEAL


Mass: 28074.807 Da / Num. of mol.: 1 / Fragment: UNP residues 437-684
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: XCC2291 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P8F1
#2: Protein Type IV fimbriae assembly protein


Mass: 12433.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: pilZ, XCC1024 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PBU4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M HEPES pH 7.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 27412 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 22.9 Å2
Reflection shellHighest resolution: 2.7 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→22.56 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 69323.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: 1. BULK SOLVENT MODEL USED 2. FRIEDEL PAIRS WERE CONSIDERED SEPARATELY AS UNIQUE REFLECTIONS IN THE CALCULATION OF THE STATISTICS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1070 4.8 %RANDOM
Rwork0.249 ---
obs0.249 22210 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.9565 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20 Å2
2--1.53 Å20 Å2
3----3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3→22.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 46 80 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.032
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg4.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it32.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.458 210 5.7 %
Rwork0.384 3463 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3C2E_paramC2E.top

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