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- PDB-4lds: The inward-facing structure of the glucose transporter from Staph... -

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Basic information

Entry
Database: PDB / ID: 4lds
TitleThe inward-facing structure of the glucose transporter from Staphylococcus epidermidis
ComponentsGlucose transporter GlcP
Keywordstransport protein / membrane protein / alpha helical transmembrane protein / glucose transporter / major facilitator superfamily
Function / homology
Function and homology information


symporter activity / plasma membrane
Similarity search - Function
: / : / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Growth Hormone; Chain: A; ...: / : / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Glucose transporter GlcP
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsChoe, J. / Aleshin, A. / Iancu, C.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of a glucose/H+ symporter and its mechanism of action.
Authors: Iancu, C.V. / Zamoon, J. / Woo, S.B. / Aleshin, A. / Choe, J.Y.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 2, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose transporter GlcP
B: Glucose transporter GlcP


Theoretical massNumber of molelcules
Total (without water)96,8152
Polymers96,8152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-17 kcal/mol
Surface area38760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.070, 118.850, 160.049
Angle α, β, γ (deg.)90.00, 100.08, 90.00
Int Tables number5
Space group name H-MI121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Glucose transporter GlcP / Glucose/H(+) symporter


Mass: 48407.477 Da / Num. of mol.: 2 / Fragment: unp residues 22-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200) (bacteria)
Strain: ATCC 12228 / FDA PCI 1200 / Gene: glcP, SE_0247 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2VG78

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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: 6.29 Å3/Da / Density % sol: 80.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% PEG 400, 0.1 M Ca Acetate, 0.1 M NaCl, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.8211 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8211 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 39873 / Num. obs: 38767 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 50.95 Å2 / Rsym value: 0.117 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2683 / Rsym value: 0.598 / % possible all: 91

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→19.902 Å / SU ML: 0.59 / σ(F): 2.36 / Phase error: 38.19 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflectionSelection details
Rfree0.3412 1946 5.02 %RANDOM
Rwork0.3018 ---
obs0.3038 38746 97.97 %-
all-39873 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→19.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6388 0 0 0 6388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146516
X-RAY DIFFRACTIONf_angle_d2.0578862
X-RAY DIFFRACTIONf_dihedral_angle_d20.572282
X-RAY DIFFRACTIONf_chiral_restr0.1631096
X-RAY DIFFRACTIONf_plane_restr0.0091064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.27980.3511400.32572426X-RAY DIFFRACTION91
3.2798-3.36810.37331230.31472649X-RAY DIFFRACTION98
3.3681-3.46670.34151310.3162634X-RAY DIFFRACTION99
3.4667-3.5780.32771430.31342603X-RAY DIFFRACTION98
3.578-3.70510.3141390.31352654X-RAY DIFFRACTION99
3.7051-3.85240.35731540.31212596X-RAY DIFFRACTION99
3.8524-4.02630.34051360.32112645X-RAY DIFFRACTION99
4.0263-4.23670.34251370.33462661X-RAY DIFFRACTION99
4.2367-4.49930.38861490.33492627X-RAY DIFFRACTION98
4.4993-4.8420.35781360.33172627X-RAY DIFFRACTION98
4.842-5.32080.35741360.33192611X-RAY DIFFRACTION97
5.3208-6.07160.34961340.3452640X-RAY DIFFRACTION98
6.0716-7.57860.38741490.34472675X-RAY DIFFRACTION99
7.5786-19.90280.29821390.2122752X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -36.4923 Å / Origin y: 56.8719 Å / Origin z: -11.196 Å
111213212223313233
T0.0274 Å20.0254 Å2-0.0857 Å2-0.2095 Å2-0.1386 Å2--0.0601 Å2
L0.031 °2-0.0043 °2-0.0322 °2-0.0063 °20.007 °2--0.0415 °2
S-0.0311 Å °-0.0636 Å °0.0241 Å °-0.0181 Å °-0.0309 Å °-0.0139 Å °-0.0009 Å °0.0314 Å °-0.154 Å °
Refinement TLS groupSelection details: all

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