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- PDB-3fjm: crystal structure of phosphate bound PEB3 -

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Basic information

Entry
Database: PDB / ID: 3fjm
Titlecrystal structure of phosphate bound PEB3
ComponentsMajor antigenic peptide PEB3
KeywordsTRANSPORT PROTEIN / PEB3 / phosphate. crystal structure
Function / homology
Function and homology information


sulfate transmembrane transport / periplasmic space
Similarity search - Function
Thiosulphate/Sulfate-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Major antigenic peptide PEB3
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMin, T. / Matte, A. / Cygler, M.
CitationJournal: Biochemistry / Year: 2009
Title: Specificity of Campylobacter jejuni adhesin PEB3 for phosphates and structural differences among its ligand complexes.
Authors: Min, T. / Vedadi, M. / Watson, D.C. / Wasney, G.A. / Munger, C. / Cygler, M. / Matte, A. / Young, N.M.
History
DepositionDec 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: Major antigenic peptide PEB3
B: Major antigenic peptide PEB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6134
Polymers55,4232
Non-polymers1902
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-22 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.417, 79.965, 98.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Major antigenic peptide PEB3


Mass: 27711.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: 11168 / Gene: Cj0289c, peb3 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): AD202 / References: UniProt: Q0PBL7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.22 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% [w/v] polyethylene glycol 3350, 0.2 M sodium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 3, 2008 / Details: Vertical and Horizontal focusing Mirrors
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→18.7 Å / Num. obs: 65094 / % possible obs: 98 % / Redundancy: 6.6 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.067 / Net I/σ(I): 15.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 8.1 / Num. unique all: 9228 / Rsym value: 0.277 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.4.0067refinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2hxw, PDB ENTRY peb3

2hxw


Resolution: 1.6→18.7 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.595 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23128 3261 5 %RANDOM
Rwork0.21667 ---
obs0.21741 61746 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 10 355 3987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0223708
X-RAY DIFFRACTIONr_angle_refined_deg0.7981.9425008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5345460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33325.122164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41615658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9811514
X-RAY DIFFRACTIONr_chiral_restr0.0640.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212774
X-RAY DIFFRACTIONr_mcbond_it0.2121.52288
X-RAY DIFFRACTIONr_mcangle_it0.40523676
X-RAY DIFFRACTIONr_scbond_it0.52331420
X-RAY DIFFRACTIONr_scangle_it0.9024.51332
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 228 -
Rwork0.244 4411 -
obs--96.85 %

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