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Basic information

Entry
Database: PDB / ID: 3ppp
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
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
TRIMETHYL GLYCINE / Glycine betaine/carnitine/choline-binding protein OpuCC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 25, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)70,2704
Polymers70,0342
Non-polymers2362
Water2,360131
1
A: Glycine betaine/carnitine/choline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1352
Polymers35,0171
Non-polymers1181
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)35,1352
Polymers35,0171
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.821, 91.782, 115.334
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-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 47.24 %
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: Nov 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 28208 / Num. obs: 28208 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.38 Å / % possible all: 92

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SW2

1sw2


Resolution: 2.4→48.8 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.804 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1212 5.1 %RANDOM
Rwork0.2165 22567 --
obs0.2183 22567 90.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.5 Å2 / Biso mean: 33.647 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 16 131 4493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224450
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9636002
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3645542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45825.619210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8615812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7741510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213336
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_it0.7671.52710
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35724360
X-RAY DIFFRACTIONr_scbond_it2.18631740
X-RAY DIFFRACTIONr_scangle_it3.484.51642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 41 -
Rwork0.257 761 -
obs--41.62 %
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)
10.92691.20740.08641.3580.18772.5993-0.03110.0056-0.2349-0.01670.0194-0.19320.00460.21080.01160.10230.02040.0110.15340.00640.177-11.5153-29.45514.9114
21.9344-0.3873-0.18980.33950.12020.55930.0335-0.0592-0.08070.0638-0.02140.02990.08070.0274-0.01210.14150.0037-0.00780.11530.01360.1352-23.0148-31.233515.1025
32.57060.1858-0.06441.6593-0.41582.8726-0.03510.3867-0.30320.0179-0.02110.11390.1336-0.34910.05620.0591-0.0015-0.02090.1864-0.05440.1257-44.2614-29.93964.2253
41.2037-0.1403-0.61680.3220.13030.72630.04080.02840.06730.0012-0.0133-0.0379-0.06510.0343-0.02750.12660.0002-0.00340.112100.1263-21.5019-22.70365.9752
50.8172-0.0022-0.53230.57130.08471.27430.0383-0.0778-0.0135-0.0052-0.03180.0117-0.0867-0.117-0.00650.14140.01-0.0160.1401-0.01470.1259-51.5491-11.920831.7635
63.9435-1.16660.10133.7199-0.41231.43720.243-0.22020.3994-0.0762-0.0439-0.2797-0.52160.1853-0.19920.243-0.05110.10160.0887-0.00350.1-35.0016-0.59220.9111
71.4366-0.1178-0.72210.61940.15431.00930.11790.0846-0.0091-0.1721-0.11310.0475-0.1363-0.1989-0.00480.13150.0518-0.04550.18430.00120.1122-55.0568-9.931723.4906
8-1.45987.3174.241146.3142-10.909116.42361.3842-1.1658-0.76091.014-0.79570.45782.9124-0.7031-0.58850.3473-0.0885-0.11870.6148-0.11070.4619-72.0345-17.635923.6509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 59
2X-RAY DIFFRACTION2A60 - 144
3X-RAY DIFFRACTION3A145 - 211
4X-RAY DIFFRACTION4A212 - 303
5X-RAY DIFFRACTION5B32 - 150
6X-RAY DIFFRACTION6B151 - 209
7X-RAY DIFFRACTION7B210 - 299
8X-RAY DIFFRACTION8B300 - 303

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