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- PDB-4c7r: Inward facing conformation of the trimeric betaine transporter Be... -

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Basic information

Entry
Database: PDB / ID: 4c7r
TitleInward facing conformation of the trimeric betaine transporter BetP in complex with lipids
ComponentsGLYCINE BETAINE TRANSPORTER BETP
KeywordsMEMBRANE PROTEIN / CHEMOSENSOR AND OSMOSENSOR / MEMBRANE / TRANSPORT / CELL MEMBRANE / SECONDARY TRANSPORTER / SODIUM COUPLED TRANSPORT / TRANSMEMBRANE / BETAINE TRANSPORT / HYPEROSMOTIC STRESS / ANIONIC LIPIDS
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
CITRATE ANION / DI(HYDROXYETHYL)ETHER / Chem-PGT / Glycine betaine transporter BetP
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKoshy, C. / Yildiz, O. / Ziegler, C.
Citation
Journal: Embo J. / Year: 2013
Title: Structural Evidence for Functional Lipid Interactions in the Betaine Transporter Betp
Authors: Koshy, C. / Schweikhard, E.S. / Gaertner, R.M. / Perez, C. / Yildiz, O. / Ziegler, C.
#1: Journal: Nature / Year: 2012
Title: Alternating-Access Mechanism in Conformationally Asymmetric Trimers of the Betaine Transporter Betp.
Authors: Perez, C. / Koshy, C. / Yildiz, O. / Ziegler, C.
History
DepositionSep 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / 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
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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: GLYCINE BETAINE TRANSPORTER BETP
B: GLYCINE BETAINE TRANSPORTER BETP
C: GLYCINE BETAINE TRANSPORTER BETP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,30123
Polymers183,0073
Non-polymers8,29420
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19490 Å2
ΔGint-197.7 kcal/mol
Surface area54580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.560, 129.500, 167.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein GLYCINE BETAINE TRANSPORTER BETP


Mass: 61002.469 Da / Num. of mol.: 3 / 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

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Non-polymers , 6 types, 78 molecules

#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT) / Phosphatidylglycerol


Mass: 751.023 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growTemperature: 291 K / pH: 5.5
Details: 100MM 3NA-CITRATE, 300MM NACL, 20% PEG 400, PH 5.5, 18 DEG CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: MARRESEARCH 165 MM / Detector: CCD / Date: Jun 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 73562 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 6.8 % / Biso Wilson estimate: 69.73 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 12.9
Reflection shellResolution: 2.65→2.8 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.39 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WIT

2wit


Resolution: 2.7→29.421 Å / SU ML: 0.41 / σ(F): 1.99 / Phase error: 29.09 / Stereochemistry target values: ML
Details: CHAIN A COMPRISES RESIDUES 56-586 CHAIN B FROM 56-552 AND CHAIN C COMPRISES RESIDUES 56-561
RfactorNum. reflection% reflection
Rfree0.2659 3485 5 %
Rwork0.2118 --
obs0.2145 69639 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.772 Å2 / ksol: 0.266 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.4622 Å20 Å20 Å2
2---20.3929 Å20 Å2
3---1.9306 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11626 0 524 58 12208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312433
X-RAY DIFFRACTIONf_angle_d0.72516845
X-RAY DIFFRACTIONf_dihedral_angle_d18.8774337
X-RAY DIFFRACTIONf_chiral_restr0.0521925
X-RAY DIFFRACTIONf_plane_restr0.0032033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7370.36151370.34742586X-RAY DIFFRACTION99
2.737-2.7760.41171390.32312627X-RAY DIFFRACTION100
2.776-2.81740.37061370.31382600X-RAY DIFFRACTION100
2.8174-2.86140.33021370.30152601X-RAY DIFFRACTION100
2.8614-2.90830.32791390.29392631X-RAY DIFFRACTION100
2.9083-2.95840.35871360.27592617X-RAY DIFFRACTION100
2.9584-3.01210.31641390.27352624X-RAY DIFFRACTION100
3.0121-3.070.35281360.25522570X-RAY DIFFRACTION99
3.07-3.13260.31461390.25132649X-RAY DIFFRACTION100
3.1326-3.20070.33181380.23722621X-RAY DIFFRACTION100
3.2007-3.2750.28461380.23432621X-RAY DIFFRACTION100
3.275-3.35680.31261390.21462632X-RAY DIFFRACTION100
3.3568-3.44740.24441380.20732610X-RAY DIFFRACTION100
3.4474-3.54870.26151370.17842625X-RAY DIFFRACTION100
3.5487-3.66310.20881400.17932655X-RAY DIFFRACTION100
3.6631-3.79370.23761380.16432626X-RAY DIFFRACTION100
3.7937-3.94530.24531410.17542665X-RAY DIFFRACTION100
3.9453-4.12440.24431390.17582642X-RAY DIFFRACTION100
4.1244-4.34120.1981410.16582669X-RAY DIFFRACTION100
4.3412-4.61220.24541400.17422657X-RAY DIFFRACTION100
4.6122-4.96670.21591400.17922666X-RAY DIFFRACTION100
4.9667-5.46370.29971410.21322673X-RAY DIFFRACTION100
5.4637-6.24770.28531420.2212699X-RAY DIFFRACTION100
6.2477-7.84660.25921440.2042749X-RAY DIFFRACTION100
7.8466-29.42280.22551500.21832839X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.8845 Å / Origin y: 16.3716 Å / Origin z: -34.377 Å
111213212223313233
T0.3015 Å2-0.083 Å20.0717 Å2-0.1846 Å2-0.0477 Å2--0.3953 Å2
L0.6256 °2-0.0785 °20.1129 °2-2.052 °2-0.1211 °2--0.6526 °2
S-0.0601 Å °0.0078 Å °-0.0464 Å °0.0762 Å °-0.0027 Å °0.2891 Å °0.1542 Å °-0.0234 Å °0.0575 Å °
Refinement TLS groupSelection details: ALL

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