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- PDB-3hia: Crystal structure of the choline binding domain of Spr1274 in Str... -

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Basic information

Entry
Database: PDB / ID: 3hia
TitleCrystal structure of the choline binding domain of Spr1274 in Streptococcus pneumoniae
ComponentsCholine binding protein
KeywordsCHOLINE-BINDING PROTEIN / beta hairpin
Function / homology
Function and homology information


Cholin Binding / 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
PHOSPHOCHOLINE / Choline binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZhang, Z.-Y. / Li, W.-Z. / Jiang, Y.-L. / Bao, R. / Zhou, C.-Z. / Chen, Y.-X.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of the choline-binding domain of Spr1274 in Streptococcus pneumoniae.
Authors: Zhang, Z. / Li, W. / Frolet, C. / Bao, R. / di Guilmi, A.M. / Vernet, T. / Chen, Y.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,05813
Polymers32,4813
Non-polymers1,57710
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Choline binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1073
Polymers10,8271
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Choline binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6606
Polymers10,8271
Non-polymers8335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Choline binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2914
Polymers10,8271
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.610, 140.610, 46.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Choline binding protein


Mass: 10826.836 Da / Num. of mol.: 3 / Fragment: choline binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: spr1274 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DP99
#2: Chemical
ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.75M (NH4)2SO4, 0.1M MES, pH 6.5, 10% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→70.36 Å / Num. obs: 15041 / Redundancy: 3.79 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.26
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.38 / Num. unique all: 2205

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V05

2v05


Resolution: 2.38→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.935 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26509 1627 12.6 %RANDOM
Rwork0.22306 ---
obs0.22852 11301 94.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.538 Å2
Baniso -1Baniso -2Baniso -3
1--6.52 Å2-3.26 Å20 Å2
2---6.52 Å20 Å2
3---9.79 Å2
Refinement stepCycle: LAST / Resolution: 2.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 52 114 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211907
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.8792603
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58925.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.215257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.408152
X-RAY DIFFRACTIONr_chiral_restr0.0950.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021501
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2791
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21237
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.591.51101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06521711
X-RAY DIFFRACTIONr_scbond_it1.36731024
X-RAY DIFFRACTIONr_scangle_it1.9664.5892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.441 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 103 -
Rwork0.335 694 -
obs--80.02 %

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