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- PDB-3ph1: The Crystal Structure of a Pathogenic Protein from the Xanthomona... -

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Basic information

Entry
Database: PDB / ID: 3ph1
TitleThe Crystal Structure of a Pathogenic Protein from the Xanthomonas campestris Reveals a New Tetrameric PilZ Domain Self-Assembled via a Unusual Helical Bundle
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / four helix bundle / PilZ domain / c-di-GMP / plant pathogen
Function / homologyCyclic di-GMP receptor, atypical PilZ domain / Atypical PilZ domain, cyclic di-GMP receptor / ACETATE ION / Cyclic di-GMP receptor atypical PilZ domain-containing protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLi, T.-N. / Chin, K.-H. / Yang, M.-D. / Chou, S.-H.
CitationJournal: To be Published
Title: The Crystal Structure of a Pathogenic Protein from the Xanthomonas campestris Reveals a New Tetrameric PilZ Domain Self-Assembled via a Unusual Helical Bundle
Authors: Li, T.-N. / Chin, K.-H. / Yang, M.-D. / Chou, S.-H.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2038
Polymers83,9674
Non-polymers2364
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-70 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.840, 89.360, 87.340
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative uncharacterized protein / PilZ protein


Mass: 20991.799 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: B100 / Gene: xcc-b100_2234 / Production host: Escherichia coli (E. coli) / References: UniProt: B0RT03
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 20% PEG 3350, pH 6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97973 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97973 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 101046 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.8 Å2
Reflection shellResolution: 2.11→2.19 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→25.02 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 500823.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED; THE SF FILE CONTAINS FRIEDEL PAIRS UNDER F_PLUS AND F_MINUS COLUMN.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4540 4.9 %RANDOM
Rwork0.229 ---
all0.24 ---
obs0.229 92998 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.0336 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20 Å21.06 Å2
2--0.42 Å20 Å2
3---2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5503 0 16 416 5935
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.691.5
X-RAY DIFFRACTIONc_mcangle_it2.892
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.982.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 672 4.9 %
Rwork0.31 12922 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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