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- PDB-2wit: CRYSTAL STRUCTURE OF THE SODIUM-COUPLED GLYCINE BETAINE SYMPORTER... -

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Basic information

Entry
Database: PDB / ID: 2wit
TitleCRYSTAL STRUCTURE OF THE SODIUM-COUPLED GLYCINE BETAINE SYMPORTER BETP FROM CORYNEBACTERIUM GLUTAMICUM WITH BOUND SUBSTRATE
ComponentsGLYCINE BETAINE TRANSPORTER BETP
KeywordsMEMBRANE PROTEIN / CHEMOSENSOR AND OSMOSENSOR / TRIMER / MEMBRANE / TRANSPORT / CELL MEMBRANE / SECONDARY TRANSPORTER / SODIUM COUPLED TRANSPORT / TRANSMEMBRANE / BETAINE TRANSPORT / HYPEROSMOTIC STRESS
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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIMETHYL GLYCINE / Glycine betaine transporter BetP
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.35 Å
AuthorsRessl, S. / Terwisscha Van Scheltinga, A.C. / Vonrhein, C. / Ott, V. / Ziegler, C.
CitationJournal: Nature / Year: 2009
Title: Molecular Basis of Transport and Regulation in the Na(+)/Betaine Symporter Betp.
Authors: Ressl, S. / Terwisscha Van Scheltinga, A.C. / Vonrhein, C. / Ott, V. / Ziegler, C.
History
DepositionMay 17, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionMay 26, 2009ID: 2W8A
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3May 13, 2015Group: Database references
Revision 1.4May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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: GLYCINE BETAINE TRANSPORTER BETP
B: GLYCINE BETAINE TRANSPORTER BETP
C: GLYCINE BETAINE TRANSPORTER BETP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,4726
Polymers185,1183
Non-polymers3543
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-24.94 kcal/mol
Surface area58370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.095, 129.422, 182.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.453, 0.007, 0.892), (0.486, 0.84, 0.24), (-0.748, 0.542, -0.384)
Vector: 110.20749, -61.97079, 143.04822)

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Components

#1: Protein GLYCINE BETAINE TRANSPORTER BETP / GLYCINE BETAINE TRANSPORTER


Mass: 61705.898 Da / Num. of mol.: 3 / Fragment: RESIDUES 30-595 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Plasmid: PASK-IBA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL-X / References: UniProt: P54582
#2: Chemical ChemComp-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12NO2
Sequence detailsAUTHOR PROVIDED ADDITIONAL SEQUENCE INFORMATION: N-TERMINAL 29 AA'S ARE DELETED, MUTATIONS E44A E45A E46A

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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: 3.2 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growTemperature: 291 K
Details: 100 MM NA3CITRATE, PH 5.55, 23% PEG400, 100 MM NACL, 18 CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97944
DetectorType: RAYONIX / Detector: CCD / Date: Feb 12, 2007
RadiationMonochromator: AL3 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 3.35→39.47 Å / Num. obs: 37151 / % possible obs: 90.7 % / Observed criterion σ(I): 1 / Redundancy: 18.9 % / Biso Wilson estimate: 27.351 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.2
Reflection shellResolution: 3.35→3.55 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1 / % possible all: 44.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHARPphasing
BUSTER-TNT2.7.0refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.35→39.47 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS IS PRESENT AND WAS USED IN THE REFINEMENT WITH LOCAL STRUCTURE SIMILARITY RESTRAINTS LSSR. SEE PDB FILE REMARK 3 NCS MODEL RESTRAINT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS IS PRESENT AND WAS USED IN THE REFINEMENT WITH LOCAL STRUCTURE SIMILARITY RESTRAINTS LSSR. SEE PDB FILE REMARK 3 NCS MODEL RESTRAINT LSSR REMARK 3 TARGET RESTRAINT LSSR SMART, O. S., M. BRANDL, C. FLENSBURG, P. KELLER, W. PACIOREK, C. VONRHEIN, AND G. BRICOGNE. 2008. REFINEMENT WITH LOCAL STRUCTURE SIMILARITY RESTRAINTS LSSR ENABLES EXPLOITATION OF INFORMATION FROM RELATED STRUCTURES AND FACILITATES USE OF NCS. PRESENTED AT THE ANNUAL MEETING OF THE AMERICAN CRYSTALLOGRAPHIC ASSOCIATION. ABSTRACT TP139, KNOXVILLE TN, U.S.A.
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 1886 5.08 %RANDOM
Rwork0.2568 ---
obs0.2572 37151 90.44 %-
Displacement parametersBiso mean: 64.34 Å2
Baniso -1Baniso -2Baniso -3
1--11.29080734 Å20 Å20 Å2
2--13.79907882 Å20 Å2
3----2.50827148 Å2
Refinement stepCycle: LAST / Resolution: 3.35→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11713 0 24 0 11737
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d120290.0022
X-RAY DIFFRACTIONt_angle_deg163480.3422
X-RAY DIFFRACTIONt_dihedral_angle_d19109.5670
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1790.0012
X-RAY DIFFRACTIONt_gen_planes18020.0065
X-RAY DIFFRACTIONt_it120080.52650
X-RAY DIFFRACTIONt_nbd430.0635
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 3.35→3.55 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2395 140 4.72 %
Rwork0.2413 2827 -
all0.2412 2967 -
obs--90.44 %

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