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- PDB-6eyq: Crystal structure of a mutated OpuBC in complex with choline -

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Basic information

Entry
Database: PDB / ID: 6eyq
TitleCrystal structure of a mutated OpuBC in complex with choline
ComponentsCholine-binding protein
KeywordsTRANSPORT PROTEIN / substrate binding protein
Function / homology
Function and homology information


cellular response to sulfate starvation / amino acid transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Osmoprotection protein (prox); domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CHOLINE ION / Choline-binding protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPeherstorfer, S. / Teichmann, L. / Smits, S.H. / Schmitt, L. / Bremer, E.
CitationJournal: To Be Published
Title: Crystal structure of a mutated OpuBC in complex with choline
Authors: Peherstorfer, S. / Teichmann, L. / Smits, S.H. / Schmitt, L. / Bremer, E.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
B: Choline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0694
Polymers68,8612
Non-polymers2082
Water12,845713
1
A: Choline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5352
Polymers34,4311
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Choline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5352
Polymers34,4311
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.659, 66.323, 126.473
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Choline-binding protein


Mass: 34430.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WE mutated D74 to Threonine
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: opuBC, proX, BSU33710 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45462
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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

Crystal growTemperature: 273 K / Method: batch mode / pH: 5 / Details: PEG3350 phosphatte buffer / PH range: 4-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.5→42.1 Å / Num. obs: 77957 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rsym value: 0.048 / Net I/σ(I): 25.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 12 / Num. unique obs: 7783 / Rsym value: 0.14 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R6U

3r6u


Resolution: 1.5→42.1 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.43
RfactorNum. reflection% reflection
Rfree0.1722 718 5 %
Rwork0.1503 --
obs0.1505 77944 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 14 713 5007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094556
X-RAY DIFFRACTIONf_angle_d1.2226171
X-RAY DIFFRACTIONf_dihedral_angle_d13.471741
X-RAY DIFFRACTIONf_chiral_restr0.071672
X-RAY DIFFRACTIONf_plane_restr0.006787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.61580.20021450.141915341X-RAY DIFFRACTION99
1.6158-1.77840.15771380.141915425X-RAY DIFFRACTION100
1.7784-2.03580.18641430.144315378X-RAY DIFFRACTION99
2.0358-2.56480.14811460.147515465X-RAY DIFFRACTION99
2.5648-42.15750.17831460.159615617X-RAY DIFFRACTION99

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