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- PDB-1r9l: structure analysis of ProX in complex with glycine betaine -

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Basic information

Entry
Database: PDB / ID: 1r9l
Titlestructure analysis of ProX in complex with glycine betaine
ComponentsGlycine betaine-binding periplasmic protein
KeywordsPROTEIN BINDING / periplasmic binding protein / cation-pi interactions / tryptophan box
Function / homology
Function and homology information


ProVWX complex / glycine import across plasma membrane / glycine betaine transport / quaternary ammonium group binding / amino acid import across plasma membrane / amino acid transport / cellular response to osmotic stress / hyperosmotic response / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex ...ProVWX complex / glycine import across plasma membrane / glycine betaine transport / quaternary ammonium group binding / amino acid import across plasma membrane / amino acid transport / cellular response to osmotic stress / hyperosmotic response / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / periplasmic space / membrane
Similarity search - Function
Glycine betaine-binding periplasmic protein; 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIMETHYL GLYCINE / Glycine betaine/proline betaine-binding periplasmic protein / Glycine betaine/proline betaine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.59 Å
AuthorsSchiefner, A. / Breed, J. / Bosser, L. / Kneip, S. / Gade, J. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E.
CitationJournal: J.BIOL.CHEM. / Year: 2004
Title: Cation-pi Interactions as Determinants for Binding of the Compatible Solutes Glycine Betaine and Proline Betaine by the Periplasmic Ligand-binding Protein ProX from Escherichia coli
Authors: Schiefner, A. / Breed, J. / Bosser, L. / Kneip, S. / Gade, J. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E.
History
DepositionOct 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Glycine betaine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8793
Polymers33,7611
Non-polymers1182
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.430, 53.900, 115.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycine betaine-binding periplasmic protein / periplasmic ligand-binding protein ProX


Mass: 33760.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: proX / Plasmid: pSK7 / Production host: Escherichia coli (E. coli) / Strain (production host): PD141 / References: UniProt: P14177, UniProt: P0AFM2*PLUS
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 1.89 Å3/Da / Density % sol: 33.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG 4000, PIPES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMTris1droppH8.3
326-28 %(w/v)PEG40001reservoir
450 mMPIPES1reservoirpH6.2-6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8439 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8439 Å / Relative weight: 1
ReflectionResolution: 1.57→15 Å / Num. all: 40866 / Num. obs: 40866 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.57→1.67 Å / % possible all: 95.2
Reflection
*PLUS
Num. measured all: 142884 / Rmerge(I) obs: 0.026
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 18.6

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
SOLVEphasing
REFMAC5.1refinement
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.59→12.26 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.186 1969 RANDOM
Rwork0.15 --
all-39378 -
obs-37409 -
Refinement stepCycle: LAST / Resolution: 1.59→12.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 9 429 2827
LS refinement shellResolution: 1.6→1.65 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.17 289 -
Rwork0.13 --
obs-2600 100 %
Refinement
*PLUS
Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.013
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.385

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