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- PDB-2rf1: Crystal structure of ChoX in an unliganded closed conformation -

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Basic information

Entry
Database: PDB / ID: 2rf1
TitleCrystal structure of ChoX in an unliganded closed conformation
ComponentsPUTATIVE GLYCINE BETAINE-BINDING ABC TRANSPORTER PROTEIN
KeywordsTRANSPORT PROTEIN / Type II binding protein / Aromatic box / ABC-transporter
Function / homology
Function and homology information


choline transport / choline binding / response to stimulus / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / periplasmic space
Similarity search - Function
Choline ABC transporter, substrate-binding protein / Glycine betaine-binding periplasmic protein; 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Choline ABC transporter, periplasmic solute-binding component
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 2 Å
AuthorsOswald, C. / Smits, S.H.J. / Hoeing, M. / Sohn-Boeser, L. / Le Rudulier, D. / Schmitt, L. / Bremer, E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structures of the choline/acetylcholine substrate-binding protein ChoX from Sinorhizobium meliloti in the liganded and unliganded-closed states.
Authors: Oswald, C. / Smits, S.H. / Hoing, M. / Sohn-Bosser, L. / Dupont, L. / Le Rudulier, D. / Schmitt, L. / Bremer, E.
History
DepositionSep 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE GLYCINE BETAINE-BINDING ABC TRANSPORTER PROTEIN
B: PUTATIVE GLYCINE BETAINE-BINDING ABC TRANSPORTER PROTEIN


Theoretical massNumber of molelcules
Total (without water)64,6042
Polymers64,6042
Non-polymers00
Water3,549197
1
A: PUTATIVE GLYCINE BETAINE-BINDING ABC TRANSPORTER PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,3021
Polymers32,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE GLYCINE BETAINE-BINDING ABC TRANSPORTER PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,3021
Polymers32,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.900, 196.200, 42.800
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PUTATIVE GLYCINE BETAINE-BINDING ABC TRANSPORTER PROTEIN


Mass: 32302.014 Da / Num. of mol.: 2 / Mutation: G251D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Gene: opuC / Production host: Escherichia coli (E. coli) / References: UniProt: Q92N37
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 277 K / pH: 5.1
Details: 0.1 Na acetate pH 5.1, 22% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.10

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.033
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 66140 / Redundancy: 3.5 % / Rmerge(I) obs: 0.104

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
SHELXrefinement
PDB_EXTRACT3data extraction
XDSdata reduction
XDSdata scaling
SHELXphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO / Resolution: 2→10 Å / Num. parameters: 41935 / Num. restraintsaints: 82311 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3286 10.3 %RANDOM
all0.201 31898 --
obs0.172 -93.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 14.861 Å2
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4573
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 0 197 4573
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.001
X-RAY DIFFRACTIONs_angle_d0.013
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.039
X-RAY DIFFRACTIONs_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.185
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.092
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.001
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.022
X-RAY DIFFRACTIONs_approx_iso_adps0.031

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