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- PDB-6jyx: Structure of CbpJ from Streptococcus Pneumoniae TIGR4 -

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Basic information

Entry
Database: PDB / ID: 6jyx
TitleStructure of CbpJ from Streptococcus Pneumoniae TIGR4
ComponentsCholine binding protein J
KeywordsCHOLINE-BINDING PROTEIN / Streptococcus pneumoniae / choline-binding proteins / adhesion
Function / homology
Function and homology information


left handed beta-beta-3-solenoid - #20 / left handed beta-beta-3-solenoid / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
CHOLINE ION / DI(HYDROXYETHYL)ETHER / Choline binding protein J
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, Q. / Zhang, J.W. / Li, Q. / Jiang, Y.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670732 China
National Natural Science Foundation of China31770787 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of the choline-binding protein CbpJ from Streptococcus pneumoniae.
Authors: Xu, Q. / Zhang, J.W. / Chen, Y. / Li, Q. / Jiang, Y.L.
History
DepositionApr 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline binding protein J
B: Choline binding protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,24518
Polymers71,5742
Non-polymers1,67116
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.523, 77.378, 187.848
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 Choline binding protein J


Mass: 35787.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: cbpJ, SP_0378 / Plasmid: pET-28a-derived / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: A0A0H2UNH0
#2: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C5H14NO
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10% PEG 20K, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 51107 / % possible obs: 93.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.259
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.199 / Num. unique obs: 1000

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V04

2v04


Resolution: 2→48.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.108 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.177 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25603 2591 5.1 %RANDOM
Rwork0.21389 ---
obs0.21603 48373 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 42.374 Å2
Baniso -1Baniso -2Baniso -3
1-4.31 Å20 Å20 Å2
2---0.82 Å20 Å2
3----3.49 Å2
Refinement stepCycle: 1 / Resolution: 2→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 112 319 5340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9157048
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33123.646277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92515751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8561521
X-RAY DIFFRACTIONr_chiral_restr0.0930.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214149
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9591.52857
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77124540
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13132332
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3374.52508
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 153 -
Rwork0.24 2712 -
obs--72.4 %

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