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- PDB-3r6u: Crystal structure of choline binding protein OpuBC from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 3r6u
TitleCrystal structure of choline binding protein OpuBC from Bacillus subtilis
ComponentsCholine-binding protein
KeywordsTRANSPORT PROTEIN / substrate binding protein / choline binding / ABC-Transporter / Choline / extracellular
Function / homology
Function and homology information


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: 1.61 Å
AuthorsPittelkow, M. / Tschapek, B. / Smits, S.H.J. / Schmitt, L. / Bremer, E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure of the Substrate-Binding Protein OpuBC from Bacillus subtilis in Complex with Choline.
Authors: Pittelkow, M. / Tschapek, B. / Smits, S.H. / Schmitt, L. / Bremer, E.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Choline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1702
Polymers32,0661
Non-polymers1041
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.900, 66.900, 64.100
Angle α, β, γ (deg.)90.00, 93.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Choline-binding protein


Mass: 32065.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / Strain: JH642 / References: UniProt: Q45462
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 8.7
Details: 20% PEG 3350, 0.2M potassium acetate, pH 8.7, VAPOR DIFFUSION, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97625
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 32793 / Num. obs: 30685 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SW2

1sw2


Resolution: 1.61→18.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.645 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21016 1583 5 %RANDOM
Rwork0.16009 ---
obs0.16263 30077 100 %-
all-32793 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.022 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.01 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.61→18.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 7 442 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222238
X-RAY DIFFRACTIONr_angle_refined_deg2.0921.9763020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60825.45599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59415419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.678156
X-RAY DIFFRACTIONr_chiral_restr0.150.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211662
X-RAY DIFFRACTIONr_mcbond_it1.2811.51360
X-RAY DIFFRACTIONr_mcangle_it2.00822194
X-RAY DIFFRACTIONr_scbond_it3.263878
X-RAY DIFFRACTIONr_scangle_it5.1614.5826
LS refinement shellResolution: 1.606→1.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 115 -
Rwork0.171 2188 -
obs--100 %

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