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Basic information

Entry
Database: PDB / ID: 3ppo
TitleStructures of the substrate-binding protein provide insights into the multiple compatible solutes binding specificities of Bacillus subtilis ABC transporter OpuC
ComponentsGlycine betaine/carnitine/choline-binding protein
KeywordsTRANSPORT PROTEIN / alpha-beta-alpha sandwich / osmoprotectant / compatible solute
Function / homology
Function and homology information


response to stress / 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
Chem-DCK / Glycine betaine/carnitine/choline-binding protein OpuCC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDu, Y. / Shi, W.W. / He, Y.X. / Yang, Y.H. / Zhou, C.Z. / Chen, Y.
CitationJournal: Biochem.J. / Year: 2011
Title: Structures of the substrate-binding protein provide insights into the multiple compatible solute binding specificities of the Bacillus subtilis ABC transporter OpuC
Authors: Du, Y. / Shi, W.W. / He, Y.X. / Yang, Y.H. / Zhou, C.Z. / Chen, Y.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: Glycine betaine/carnitine/choline-binding protein
B: Glycine betaine/carnitine/choline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3584
Polymers70,0342
Non-polymers3242
Water2,306128
1
A: Glycine betaine/carnitine/choline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1792
Polymers35,0171
Non-polymers1621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycine betaine/carnitine/choline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1792
Polymers35,0171
Non-polymers1621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.890, 91.070, 115.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Glycine betaine/carnitine/choline-binding protein / OpuCC / Osmoprotectant-binding protein


Mass: 35016.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: opuCC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32243
#2: Chemical ChemComp-DCK / (2S)-3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium / D-carnitine / Carnitine


Mass: 162.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28%(v/v) Polyethylene Glycol 400, 0.2M Calcium Chloride dihydrate, 0.1M HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 19559 / Num. obs: 19559 / % possible obs: 94.2 %
Reflection shellResolution: 2.6→2.74 Å / % possible all: 83.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SW2
Resolution: 2.7→29.92 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.867 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.217 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 739 5.1 %RANDOM
Rwork0.2122 13838 --
obs0.2135 13838 78.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 30 Å2 / Biso mean: 27.961 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---1.75 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 22 128 4496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9646010
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.63825.619210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41315812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5631510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213344
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it0.4021.52696
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71624348
X-RAY DIFFRACTIONr_scbond_it1.07431760
X-RAY DIFFRACTIONr_scangle_it1.7784.51662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 5 -
Rwork0.285 131 -
obs--10.25 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.17940.31191.15661.79050.83842.2133-0.1026-0.03640.22120.05160.08450.1497-0.1765-0.07280.01820.11570.02040.03390.23190.02340.1298-17.621733.75897.0394
21.6934-0.54590.01870.6002-0.41670.8349-0.0555-0.043-0.01940.02740.0681-0.06410.07320.0741-0.01260.1085-0.00850.00920.1756-0.00830.12841.30926.534814.4137
31.630.68570.77872.78011.09941.0313-0.08360.36220.2695-0.0939-0.0210.073-0.32510.17090.10460.1858-0.00860.01690.28830.07090.188810.88733.12424.8854
41.46050.2663-0.02260.4621-0.67061.65450.0450.14370.01510.0026-0.0928-0.09790.01970.1870.04790.0633-0.00230.01410.18880.0190.10562.26224.80677.1685
528.2341-2.2785-5.52938.29021.93995.0913-0.633-1.09940.77190.46410.08510.7328-0.0184-0.76840.54790.27960.1020.08050.4058-0.05960.3299-27.516833.392618.5656
61.3898-0.2763-0.00441.6464-0.8422.04220.09910.1492-0.36460.0471-0.08390.12870.1208-0.1128-0.01520.0932-0.0194-0.00770.219-0.0210.1899-16.200320.0932.526
70.47050.0293-1.15362.30670.01212.91320.0538-0.0735-0.06870.3068-0.1511-0.273-0.01960.16070.09730.1789-0.0056-0.04910.290.08160.16430.40767.60535.1781
81.3189-0.16091.30050.9638-0.21962.7647-0.0802-0.06050.12790.06960.04180.0085-0.05320.04660.03840.096-0.02070.02170.20060.00690.1216.460716.362233.673
91.4965-0.57210.41182.80.33783.27160.09230.0501-0.2892-0.3124-0.17110.15950.2833-0.23770.07880.1395-0.04420.00290.27150.01480.16273.20821.51516.347
101.66810.29320.46020.58970.09970.43820.1110.0984-0.0757-0.0979-0.12880.07460.2429-0.0290.01790.18530.0046-0.00910.26530.01720.1059.88853.729920.4324
112.2025-0.20880.12673.36311.79143.4999-0.06350.02960.0737-0.06690.0339-0.33780.14340.28060.02960.0389-0.00530.03970.24640.05910.148531.955111.272526.6754
1220.57911.97765.36552.17727.564127.8352.34050.19341.0039-0.5597-0.4503-0.6349-1.9474-0.2017-1.89020.69120.27420.49030.94650.46120.653940.160716.331721.7824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 88
2X-RAY DIFFRACTION2A89 - 161
3X-RAY DIFFRACTION3A162 - 208
4X-RAY DIFFRACTION4A209 - 250
5X-RAY DIFFRACTION5A251 - 255
6X-RAY DIFFRACTION6A256 - 303
7X-RAY DIFFRACTION7B32 - 76
8X-RAY DIFFRACTION8B77 - 140
9X-RAY DIFFRACTION9B141 - 179
10X-RAY DIFFRACTION10B180 - 248
11X-RAY DIFFRACTION11B249 - 297
12X-RAY DIFFRACTION12B298 - 303

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