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- PDB-2hxw: Crystal Structure of Peb3 from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 2hxw
TitleCrystal Structure of Peb3 from Campylobacter jejuni
ComponentsMajor antigenic peptide PEB3
Keywordsperiplasmic binding protein / Peb3 / N-glycosylation / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
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
CITRATE ANION / Major antigenic peptide PEB3 / :
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsRangarajan, E.S. / Bhatia, S. / Watson, D.C. / Munger, C. / Cygler, M. / Matte, A. / Young, N.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Protein Sci. / Year: 2007
Title: Structural context for protein N-glycosylation in bacteria: The structure of PEB3, an adhesin from Campylobacter jejuni.
Authors: Rangarajan, E.S. / Bhatia, S. / Watson, D.C. / Munger, C. / Cygler, M. / Matte, A. / Young, N.M.
History
DepositionAug 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)53,4624
Polymers53,0842
Non-polymers3782
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-5 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.472, 101.672, 59.099
Angle α, β, γ (deg.)90.00, 108.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Major antigenic peptide PEB3


Mass: 26541.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: peb3 / Plasmid: pCWori+ / Production host: Escherichia coli (E. coli) / Strain (production host): AD202 / References: UniProt: Q9PIK7, UniProt: Q0PBL7*PLUS
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 3350, 0.2M diammonium hydrogen citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2006
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 70409 / Num. obs: 69829 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.056
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.332 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.556 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21223 3373 5 %RANDOM
Rwork0.18702 ---
all0.2 67978 --
obs0.1883 64605 99.57 %-
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: 26.926 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å2-1.21 Å2
2---1.09 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 26 349 4003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223730
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9475048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5355468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63325.244164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53815661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8111513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022805
X-RAY DIFFRACTIONr_nbd_refined0.1950.21805
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2315
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.212
X-RAY DIFFRACTIONr_mcbond_it0.7061.52340
X-RAY DIFFRACTIONr_mcangle_it1.15423697
X-RAY DIFFRACTIONr_scbond_it1.74331583
X-RAY DIFFRACTIONr_scangle_it2.7814.51345
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 217 -
Rwork0.207 4767 -
obs--99.56 %

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