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- PDB-3p03: Crystal structure of BetP-G153D with choline bound -

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Basic information

Entry
Database: PDB / ID: 3p03
TitleCrystal structure of BetP-G153D with choline bound
ComponentsGlycine betaine transporter BetP
KeywordsTRANSPORT PROTEIN / Secondary transporter
Function / homology
Function and homology information


nitrogen compound transport / symporter activity / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
BCCT transporter family / BCCT transporter, conserved site / BCCT, betaine/carnitine/choline family transporter / BCCT family of transporters signature.
Similarity search - Domain/homology
CHOLINE ION / Glycine betaine transporter BetP
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å
AuthorsPerez, C. / Ressl, S. / Ziegler, Z.
CitationJournal: Embo J. / Year: 2011
Title: Substrate specificity and ion coupling in the Na(+)/betaine symporter BetP.
Authors: Perez, C. / Koshy, C. / Ressl, S. / Nicklisch, S. / Kramer, R. / Ziegler, C.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: 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 / 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 transporter BetP
B: Glycine betaine transporter BetP
C: Glycine betaine transporter BetP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2864
Polymers183,1823
Non-polymers1041
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-27 kcal/mol
Surface area59770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.560, 129.310, 183.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycine betaine transporter BetP


Mass: 61060.508 Da / Num. of mol.: 3 / Fragment: UNP residues 30-595 / Mutation: E44A, E45A, E46A, G153D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: betP, Cgl0892, cg1016 / Plasmid: pASK-IBA7 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alfa / References: UniProt: P54582
#2: Chemical ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO

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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: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 5.5
Details: 22% PEG 400, 100 mM NaCl, 100 mM Na3Citrate, 5 mM Choline, pH 5.5, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2009
RadiationMonochromator: AL3 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→46.2 Å / Num. obs: 42602 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 101.254 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 14.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.3-3.50.7173.1784106812100
3.5-3.80.4535.2964117722100
3.8-4.50.2510.91738941100799.9
4.5-60.13120.41541949750100
6-80.09330634234193100
8-100.07537.7222571517100
10-150.06837.4161321158100
15-350.05831.2448143390.2
35-460.0517.8391020.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.05 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.48 Å34.75 Å
Translation3.48 Å34.75 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→46.2 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7817 / SU ML: 0.43 / σ(F): 1.99 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3004 3705 9.95 %
Rwork0.2446 33514 -
obs0.2502 37219 91.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.407 Å2 / ksol: 0.273 e/Å3
Displacement parametersBiso max: 560.78 Å2 / Biso mean: 107.8704 Å2 / Biso min: 3.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.196 Å20 Å2-0 Å2
2--3.8118 Å2-0 Å2
3----3.6158 Å2
Refinement stepCycle: LAST / Resolution: 3.35→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11342 0 7 0 11349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711771
X-RAY DIFFRACTIONf_angle_d1.1116034
X-RAY DIFFRACTIONf_chiral_restr0.0691865
X-RAY DIFFRACTIONf_plane_restr0.0041972
X-RAY DIFFRACTIONf_dihedral_angle_d18.1573890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.35-3.46970.31091170.28191053117029
3.4697-3.60860.3433170.25293014333183
3.6086-3.77280.29443960.239136384034100
3.7728-3.97160.27973970.223236464043100
3.9716-4.22020.28753880.21436564044100
4.2202-4.54580.29014080.22536314039100
4.5458-5.00280.28564070.232136714078100
5.0028-5.72560.32444330.254536704103100
5.7256-7.20920.32843930.262837504143100
7.2092-46.20.274490.24263785423498
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)
10.5838-0.1415-0.23930.6325-0.10840.13790.1925-0.26660.04481.0093-0.01110.6322-0.2008-0.0570.20081.10160.10940.7240.2771-0.04750.4422-17.75139.002977.9343
20.37570.20070.13320.20870.18860.24970.2726-0.37360.29160.2795-0.46360.17570.24050.0155-0.15461.3269-0.20790.8970.2978-0.1780.5761-17.389512.829375.3136
30.2179-0.0376-0.1470.0760.08260.1340.2410.1080.05610.093-0.2250.1879-0.1561-0.28040.11830.3156-0.02880.470.8136-0.26241.1211-37.386120.496281.7728
40.9351-0.0874-0.06411.3717-0.65150.4084-0.2325-0.71320.13021.35050.01260.7513-0.0754-0.0575-0.38011.0698-0.17630.85870.385-0.07940.5552-22.303716.652773.2269
50.8805-0.04870.27680.37790.33160.62830.08110.218-0.2142-0.531-0.05030.2386-0.29450.3229-0.02270.803-0.06150.06110.18220.10410.2618-0.1814-19.028136.0895
60.3694-0.28380.12970.4668-0.20830.34490.0102-0.0536-0.278-0.35840.08840.42410.2939-0.2419-0.08210.1493-0.3574-0.1450.4269-0.15340.9055-30.497424.220332.6736
70.54470.09880.79881.70050.13521.16570.174-0.1806-0.0855-0.6757-0.1821.0816-0.0131-0.62790.18760.3003-0.0193-0.34090.3089-0.14390.7983-25.621428.491833.4725
80.0742-0.1194-0.24390.17940.38230.78660.0940.2353-0.16890.0909-0.16650.09150.469-0.30140.06920.5602-0.1068-0.5690.83140.17780.6892-24.321131.951112.5273
90.3604-0.31430.32120.89620.25670.6495-0.09540.159-0.1916-0.5279-0.21820.797-0.1121-0.24070.15290.43260.0601-0.29280.3214-0.27550.5364-20.641831.073430.9425
100.1360.07170.02720.12260.01990.0056-0.008-0.0332-0.0679-0.03070.17380.01630.01080.0196-0.07241.1359-0.6506-0.20941.66930.26930.8-31.9943-6.526443.379
110.0341-0.05080.21916.6397-2.68412.70670.182-0.05140.2143-0.4046-0.9662-1.74550.04280.92140.2833-0.0045-0.0027-0.03550.3055-0.02030.480824.361722.790636.3407
120.56870.24360.51422.624-0.14651.22460.09090.1651-0.11120.4822-0.3144-0.88490.02420.41220.25370.1871-0.0313-0.07040.14450.11810.24778.964710.90650.2034
130.1071-0.21790.23782.4655-1.13441.392-0.27930.03190.30.8144-0.5217-1.3774-0.21090.5880.06610.209-0.1729-0.34260.39630.1450.75619.214318.227453.1869
140.1616-0.0036-0.17793.264-0.27970.41390.2807-0.06940.07430.7985-0.3417-1.67680.01440.44280.2366-0.06840.0764-0.30690.18140.21240.803519.24714.699951.9716
150.04590.01940.15471.4147-0.5520.7863-0.1781-0.06990.08610.0121-0.24870.0349-0.2784-0.22040.37440.24630.3766-0.37890.8019-0.43850.7885-15.3734-9.725634.1159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 57:154)A57 - 154
2X-RAY DIFFRACTION2(chain A and resid 155:259)A155 - 259
3X-RAY DIFFRACTION3(chain A and resid 260:325)A260 - 325
4X-RAY DIFFRACTION4(chain A and resid 326:553)A326 - 553
5X-RAY DIFFRACTION5(chain A and resid 554:589)A554 - 589
6X-RAY DIFFRACTION6(chain B and resid 57:151)B57 - 151
7X-RAY DIFFRACTION7(chain B and resid 152:271)B152 - 271
8X-RAY DIFFRACTION8(chain B and resid 272:311)B272 - 311
9X-RAY DIFFRACTION9(chain B and resid 312:546)B312 - 546
10X-RAY DIFFRACTION10(chain B and resid 547:558)B547 - 558
11X-RAY DIFFRACTION11(chain C and resid 57:109)C57 - 109
12X-RAY DIFFRACTION12(chain C and resid 110:223)C110 - 223
13X-RAY DIFFRACTION13(chain C and resid 224:373)C224 - 373
14X-RAY DIFFRACTION14(chain C and resid 374:548)C374 - 548
15X-RAY DIFFRACTION15(chain C and resid 549:568)C549 - 568

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