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- PDB-2rej: ABC-transporter choline binding protein in unliganded semi-closed... -

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Basic information

Entry
Database: PDB / ID: 2rej
TitleABC-transporter choline binding protein in unliganded semi-closed conformation
ComponentsPUTATIVE GLYCINE BETAINE ABC TRANSPORTER PROTEIN
KeywordsCHOLINE-BINDING PROTEIN / Type II binding protein / Aromatic box / ABC-transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


choline transport / choline binding / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 26, 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
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,6042
Polymers64,6042
Non-polymers00
Water00
1
A: PUTATIVE GLYCINE BETAINE ABC TRANSPORTER PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,3021
Polymers32,3021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE GLYCINE BETAINE ABC TRANSPORTER PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,3021
Polymers32,3021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.100, 232.500, 47.300
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211
Details2 biological units in the asymmetric unit

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Components

#1: Protein PUTATIVE GLYCINE BETAINE 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
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Na acetate pH 5.0, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 22282 / Redundancy: 3.4 % / Rmerge(I) obs: 0.222

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0003refinement
PDB_EXTRACT3data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.767 / SU B: 26.351 / SU ML: 0.537 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.85 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Twinning operator is h,-k,-l. Twinning perfect pseudo-merohedral twin.
RfactorNum. reflection% reflectionSelection details
Rfree0.35867 1158 5.2 %RANDOM
Rwork0.29563 ---
obs0.29889 21123 98.92 %-
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: 31.398 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å2-0.46 Å2
2---1.28 Å20 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 0 0 4352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9526022
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9835574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.81326.105190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34615740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6981512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023354
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21209
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.22883
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0710.22
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_it0.1731.52935
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.31124550
X-RAY DIFFRACTIONr_scbond_it0.30731738
X-RAY DIFFRACTIONr_scangle_it0.4874.51472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 76 -
Rwork0.261 1580 -
obs--98.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44070.0902-0.16171.4411-0.23151.08590.0311-0.0608-0.33510.1418-0.0132-0.0530.1020.0209-0.0179-0.0404-0.0256-0.0128-0.0360.0363-0.025716.251-9.02216.07
20.91360.25610.21981.8065-0.52891.459-0.01770.02890.0783-0.0890.0211-0.005-0.1916-0.0798-0.0033-0.0336-0.01360.01240.01140.0153-0.086215.27214.4850.559
30.77590.44240.57182.28220.35443.0136-0.23350.07160.2677-0.2776-0.0950.0979-0.50170.06360.3285-0.0093-0.0005-0.0646-0.08310.0042-0.03422.332-37.2674.912
41.5806-0.42-0.01912.2816-0.36332.0747-0.0768-0.0617-0.12970.0794-0.06810.06590.2335-0.10250.1449-0.0743-0.00820.0336-0.0528-0.0339-0.08470.255-60.89120.398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 1144 - 87
2X-RAY DIFFRACTION1AA235 - 314208 - 287
3X-RAY DIFFRACTION2AA120 - 23093 - 203
4X-RAY DIFFRACTION3BB31 - 1144 - 87
5X-RAY DIFFRACTION3BB235 - 314208 - 287
6X-RAY DIFFRACTION4BB120 - 23093 - 203

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