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- PDB-3chg: The compatible solute-binding protein OpuAC from Bacillus subtili... -

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Basic information

Entry
Database: PDB / ID: 3chg
TitleThe compatible solute-binding protein OpuAC from Bacillus subtilis in complex with DMSA
ComponentsGlycine betaine-binding protein
KeywordsLIGAND BINDING PROTEIN / Transport protein / substrate binding protein
Function / homology
Function and homology information


amino acid transport / response to stimulus / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / membrane raft
Similarity search - Function
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 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(dimethyl-lambda~4~-sulfanyl)acetic acid / Glycine betaine-binding protein OpuAC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSmits, S.H.J. / Hoing, M. / Lecher, J. / Jebbar, M. / Schmitt, L. / Bremer, E.
CitationJournal: J.Bacteriol. / Year: 2008
Title: The Compatible-Solute-Binding Protein OpuAC from Bacillus subtilis: Ligand Binding, Site-Directed Mutagenesis, and Crystallographic Studies
Authors: Smits, S.H.J. / Hoing, M. / Lecher, J. / Jebbar, M. / Schmitt, L. / Bremer, E.
History
DepositionMar 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
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_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

Downloads & links

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Assembly

Deposited unit
D: Glycine betaine-binding protein
A: Glycine betaine-binding protein
B: Glycine betaine-binding protein
C: Glycine betaine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6128
Polymers119,1244
Non-polymers4894
Water0
1
D: Glycine betaine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9032
Polymers29,7811
Non-polymers1221
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Glycine betaine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9032
Polymers29,7811
Non-polymers1221
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Glycine betaine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9032
Polymers29,7811
Non-polymers1221
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Glycine betaine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9032
Polymers29,7811
Non-polymers1221
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.508, 150.606, 58.959
Angle α, β, γ (deg.)90.00, 104.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycine betaine-binding protein


Mass: 29780.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: opuAC / Plasmid: Pbkb76 OpuAC_wt / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P46922
#2: Chemical
ChemComp-313 / (dimethyl-lambda~4~-sulfanyl)acetic acid


Mass: 122.186 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S

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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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 274 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: Tris, ammonium acetate, PEG 4000, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 274K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.97854 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 24818 / Num. obs: 20667 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.164
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.56 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.766 / SU B: 28.413 / SU ML: 0.55 / Cross valid method: THROUGHOUT / ESU R Free: 0.659 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35947 1119 5.1 %RANDOM
Rwork0.28528 ---
obs0.28902 20666 93.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.676 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.07 Å2
2--0.06 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8076 0 28 0 8104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228315
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.95811233
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0651036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.85325.81315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.611151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0861512
X-RAY DIFFRACTIONr_chiral_restr0.0730.21240
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026028
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.24095
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25559
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1971.55312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.34728300
X-RAY DIFFRACTIONr_scbond_it0.39633569
X-RAY DIFFRACTIONr_scangle_it0.6244.52933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 65 -
Rwork0.365 1548 -
obs--96.59 %

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