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- PDB-2wsx: Crystal Structure of Carnitine Transporter from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2wsx
TitleCrystal Structure of Carnitine Transporter from Escherichia coli
ComponentsL-CARNITINE/GAMMA-BUTYROBETAINE ANTIPORTER
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


(R)-carnitine:4-(trimethylammonio)butanoate antiporter activity / 4-(trimethylammonio)butanoate transport / carnitine transport / carnitine transmembrane transporter activity / carnitine metabolic process / transmembrane transporter activity / plasma membrane
Similarity search - Function
L-carnitine/gamma-butyrobetaine antiporter CaiT / BCCT transporter family / BCCT transporter, conserved site / BCCT, betaine/carnitine/choline family transporter / BCCT family of transporters signature.
Similarity search - Domain/homology
3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM / L-carnitine/gamma-butyrobetaine antiporter
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSchulze, S. / Terwisscha van Scheltinga, A.C. / Kuehlbrandt, W.
CitationJournal: Nature / Year: 2010
Title: Structural Basis of Na(+)-Independent and Cooperative Substrate/Product Antiport in Cait.
Authors: Schulze, S. / Koster, S. / Geldmacher, U. / Terwisscha Van Scheltinga, A.C. / Kuhlbrandt, W.
History
DepositionSep 10, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: L-CARNITINE/GAMMA-BUTYROBETAINE ANTIPORTER
B: L-CARNITINE/GAMMA-BUTYROBETAINE ANTIPORTER
C: L-CARNITINE/GAMMA-BUTYROBETAINE ANTIPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,7919
Polymers169,9143
Non-polymers8776
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-36.5 kcal/mol
Surface area55690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.200, 124.200, 154.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESID 1504
211CHAIN B AND RESID 1504
311CHAIN C AND RESID 1504
112CHAIN A AND RESID 1505
212CHAIN B AND RESID 1505
312CHAIN C AND RESID 1505
113CHAIN A
213CHAIN B
313CHAIN C

NCS ensembles :
ID
1
2
3

NCS oper: (Code: given
Matrix: (-0.450035, -0.814944, 0.365149), (0.875963, -0.482368, 0.003042), (0.173656, 0.321226, 0.930944)
Vector: 51.4352, -18.7749, -7.46858)

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Components

#1: Protein L-CARNITINE/GAMMA-BUTYROBETAINE ANTIPORTER / L-CARNITINE-G-BUTYROBETAINE ANTIPORTER


Mass: 56637.855 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P31553
#2: Chemical
ChemComp-NM2 / 3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM


Mass: 146.207 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H16NO2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→24.7 Å / Num. obs: 71232 / % possible obs: 97.7 % / Observed criterion σ(I): 1.3 / Redundancy: 1.9 % / Biso Wilson estimate: 147.63 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 3.4→3.6 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.3 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→24.676 Å / SU ML: 1.12 / σ(F): 1.01 / Phase error: 29.15 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2711 3357 5 %
Rwork0.2373 --
obs0.239 66982 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.286 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.23 Å20 Å20 Å2
2--7.23 Å20 Å2
3----14.46 Å2
Refinement stepCycle: LAST / Resolution: 3.5→24.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11703 0 60 0 11763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112138
X-RAY DIFFRACTIONf_angle_d1.30216608
X-RAY DIFFRACTIONf_dihedral_angle_d18.1244029
X-RAY DIFFRACTIONf_chiral_restr0.0771902
X-RAY DIFFRACTIONf_plane_restr0.0061983
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A10X-RAY DIFFRACTIONPOSITIONAL
12B10X-RAY DIFFRACTIONPOSITIONAL0.038
13C10X-RAY DIFFRACTIONPOSITIONAL0.041
21A10X-RAY DIFFRACTIONPOSITIONAL
22B10X-RAY DIFFRACTIONPOSITIONAL0.023
23C10X-RAY DIFFRACTIONPOSITIONAL0.017
31A3901X-RAY DIFFRACTIONPOSITIONAL
32B3901X-RAY DIFFRACTIONPOSITIONAL0.053
33C3901X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.54990.32731460.33652680X-RAY DIFFRACTION100
3.5499-3.60270.35231620.332662X-RAY DIFFRACTION100
3.6027-3.65880.34641250.30722674X-RAY DIFFRACTION100
3.6588-3.71860.3551040.30112596X-RAY DIFFRACTION100
3.7186-3.78250.29511260.29332782X-RAY DIFFRACTION100
3.7825-3.8510.30581440.28612606X-RAY DIFFRACTION100
3.851-3.92480.26471700.28372615X-RAY DIFFRACTION100
3.9248-4.00460.34461300.27532714X-RAY DIFFRACTION100
4.0046-4.09130.30761220.26252586X-RAY DIFFRACTION100
4.0913-4.1860.25011240.24472710X-RAY DIFFRACTION100
4.186-4.29020.28931580.2482638X-RAY DIFFRACTION100
4.2902-4.40560.30821440.24142668X-RAY DIFFRACTION100
4.4056-4.53440.29531520.24382618X-RAY DIFFRACTION100
4.5344-4.67980.25161300.22282620X-RAY DIFFRACTION100
4.6798-4.84590.27061340.21762726X-RAY DIFFRACTION100
4.8459-5.03830.25681800.22552622X-RAY DIFFRACTION100
5.0383-5.26550.23991440.23262626X-RAY DIFFRACTION100
5.2655-5.54020.31211380.25682628X-RAY DIFFRACTION100
5.5402-5.88290.32831500.23982688X-RAY DIFFRACTION100
5.8829-6.330.30651500.23382636X-RAY DIFFRACTION100
6.33-6.9540.28581500.21552664X-RAY DIFFRACTION100
6.954-7.93090.21661240.18932656X-RAY DIFFRACTION100
7.9309-9.88410.18041120.15652690X-RAY DIFFRACTION100
9.8841-24.67660.2471380.252520X-RAY DIFFRACTION95

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