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- PDB-3dsg: XC1028 from Xanthomonas campestris Adopts a PilZ Domain-like Stru... -

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Basic information

Entry
Database: PDB / ID: 3dsg
TitleXC1028 from Xanthomonas campestris Adopts a PilZ Domain-like Structure Yet with Trivial c-di-GMP Binding Activity
ComponentsType IV fimbriae assembly protein
KeywordsUNKNOWN FUNCTION / PilZ domain / Xanthomonas campestris / c-di-GMP / type IV pilus / PA2960
Function / homologypredicted glycosyltransferase like domains / PilZ domain / PilZ domain / cyclic-di-GMP binding / Thrombin, subunit H / Beta Barrel / Mainly Beta / Type IV fimbriae assembly protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsLi, T.N. / Chin, K.H. / Liu, J.H. / Wang, A.H.J. / Chou, S.H.
CitationJournal: Proteins / Year: 2009
Title: XC1028 from Xanthomonas campestris adopts a PilZ domain-like structure without a c-di-GMP switch.
Authors: Li, T.N. / Chin, K.H. / Liu, J.H. / Wang, A.H. / Chou, S.H.
History
DepositionJul 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type IV fimbriae assembly protein
B: Type IV fimbriae assembly protein
C: Type IV fimbriae assembly protein


Theoretical massNumber of molelcules
Total (without water)31,6473
Polymers31,6473
Non-polymers00
Water2,270126
1
A: Type IV fimbriae assembly protein


Theoretical massNumber of molelcules
Total (without water)10,5491
Polymers10,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type IV fimbriae assembly protein


Theoretical massNumber of molelcules
Total (without water)10,5491
Polymers10,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Type IV fimbriae assembly protein


Theoretical massNumber of molelcules
Total (without water)10,5491
Polymers10,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.896, 50.962, 92.745
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number5
Space group name H-MC121
DetailsC2

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Components

#1: Protein Type IV fimbriae assembly protein


Mass: 10548.862 Da / Num. of mol.: 3 / Fragment: PilZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8PBU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 18% PEG 2KMME, 2% glycerol, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97920, 0.96398, 0.97888
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 5, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.963981
30.978881
ReflectionResolution: 2.09→30 Å / Num. obs: 22930 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.22 / Net I/σ(I): 27.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1714 / Rsym value: 0.23 / % possible all: 79

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.09→25.48 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 235091.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3802 9 %RANDOM
Rwork0.277 ---
obs0.277 22930 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.691 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1-17.79 Å20 Å2-1.45 Å2
2--11.58 Å20 Å2
3----29.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.09→25.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 0 126 2263
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.04
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_deg4.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d6.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2→2.13 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.421 901 -
obs--9.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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