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- PDB-3dh4: Crystal Structure of Sodium/Sugar symporter with bound Galactose ... -

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Basic information

Entry
Database: PDB / ID: 3dh4
TitleCrystal Structure of Sodium/Sugar symporter with bound Galactose from vibrio parahaemolyticus
ComponentsSodium/glucose cotransporter
KeywordsTRANSPORT PROTEIN / Membrane protein / symporter / sugar transport / SGLT / Ion transport / Membrane / Sodium transport / Symport / Transmembrane / Transport
Function / homology
Function and homology information


symporter activity / sodium ion transport / carbohydrate transport / plasma membrane
Similarity search - Function
Sodium/glucose cotransporter / Sodium/glucose cotransporter / Sodium:solute symporter family signature 1. / Sodium/solute symporter, conserved site / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ERBIUM (III) ION / beta-D-galactopyranose / Sodium/glucose cotransporter
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsAbramson, J. / Faham, S. / Cascio, D.
CitationJournal: Science / Year: 2008
Title: The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport.
Authors: Faham, S. / Watanabe, A. / Besserer, G.M. / Cascio, D. / Specht, A. / Hirayama, B.A. / Wright, E.M. / Abramson, J.
History
DepositionJun 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/glucose cotransporter
B: Sodium/glucose cotransporter
C: Sodium/glucose cotransporter
D: Sodium/glucose cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,21716
Polymers227,7364
Non-polymers1,48212
Water0
1
A: Sodium/glucose cotransporter
B: Sodium/glucose cotransporter
hetero molecules

C: Sodium/glucose cotransporter
D: Sodium/glucose cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,21716
Polymers227,7364
Non-polymers1,48212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area9260 Å2
ΔGint-55 kcal/mol
Surface area78190 Å2
MethodPISA
2
A: Sodium/glucose cotransporter
B: Sodium/glucose cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6098
Polymers113,8682
Non-polymers7416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-31 kcal/mol
Surface area39550 Å2
MethodPISA
3
C: Sodium/glucose cotransporter
D: Sodium/glucose cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6098
Polymers113,8682
Non-polymers7416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-31 kcal/mol
Surface area39570 Å2
MethodPISA
4
A: Sodium/glucose cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4725
Polymers56,9341
Non-polymers5384
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Sodium/glucose cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1373
Polymers56,9341
Non-polymers2032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
C: Sodium/glucose cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1373
Polymers56,9341
Non-polymers2032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
D: Sodium/glucose cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4725
Polymers56,9341
Non-polymers5384
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.280, 109.210, 127.580
Angle α, β, γ (deg.)109.70, 92.02, 102.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: UNK / Beg label comp-ID: UNK / End auth comp-ID: NA / End label comp-ID: NA / Refine code: 1 / Auth seq-ID: 3 - 801 / Label seq-ID: 1

Dom-IDAuth asym-IDLabel asym-ID
1AA - H
2BB - J
3CC - L
4DD - P

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Components

#1: Protein
Sodium/glucose cotransporter / Na(+)/glucose symporter


Mass: 56933.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: sglT / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: P96169
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-ER3 / ERBIUM (III) ION / Erbium


Mass: 167.259 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Er
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
Sequence detailsTHE FULL-LENGHT PROTEIN (RESIDUES 1-543) WAS CRYSTALLIZED. THE N-TERMINAL REGION 1-46 WAS NOT ...THE FULL-LENGHT PROTEIN (RESIDUES 1-543) WAS CRYSTALLIZED. THE N-TERMINAL REGION 1-46 WAS NOT MODELED DUE TO LACK OF ELECTRON DENSITY EXCEPT FOR RESIDUES 3-19 WHICH WERE MODELED AS ALANINES AND ARE REFERRED TO AS UNK (UNKNOWN) IN THE COORDINATES AND SEQRES RECORDS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.88 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes, 200mM Ca Acetate, 20-25% PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9793
SYNCHROTRONAPS 23-ID-D20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 25, 2008
MARMOSAIC 300 mm CCD2CCDFeb 17, 2008
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 103009 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 8.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.55 / % possible all: 69.9

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 1 / SU B: 29.93 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues 3-19 from each chain are build as polyala. Electron density in this region (3-19) lacks the clarity required to identify these ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues 3-19 from each chain are build as polyala. Electron density in this region (3-19) lacks the clarity required to identify these side chains reliably. DATA FILE SUBMITTED INCLUDES (1) INITIAL DATA AND (2) DATA AFTER ANISOTROPIC TRUNCATION AND B CORRECTION. SET (2) WAS USED FOR REFINEMENT. DATA WAS TRUNCATED BEFORE REFINEMENT WITH THE ANISOTROPY SERVER: (HTTP://WWW.DOE-MBI.UCLA.EDU/~SAWAYA/ANISOSCALE/).
RfactorNum. reflection% reflectionSelection details
Rfree0.28715 2998 5 %RANDOM
Rwork0.26979 ---
obs0.27063 57175 53.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.531 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.26 Å2-0.61 Å2
2--0.19 Å20.06 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15416 0 56 0 15472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02215852
X-RAY DIFFRACTIONr_bond_other_d00.0210032
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.95721648
X-RAY DIFFRACTIONr_angle_other_deg4.3792.99524672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79652036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83423.902492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.479152424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1331512
X-RAY DIFFRACTIONr_chiral_restr0.0610.22620
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117356
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023268
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9491.510148
X-RAY DIFFRACTIONr_mcbond_other0.1381.54172
X-RAY DIFFRACTIONr_mcangle_it1.819216280
X-RAY DIFFRACTIONr_scbond_it2.30335716
X-RAY DIFFRACTIONr_scangle_it2.4674.55368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6375 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.020.05
2Btight positional0.020
3Ctight positional0.020
4Dtight positional0.020
1Atight thermal0.410.5
2Btight thermal0.350
3Ctight thermal0.260
4Dtight thermal0.220
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.049 2 -
Rwork0.258 101 -
obs--1.23 %
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)
12.1933-0.31720.49613.52650.98581.78470.21250.0960.4145-0.7553-0.19290.149-0.33440.0022-0.01960.1522-0.03090.1256-0.06580.1278-0.005528.1676-43.141559.5122
24.5131-1.93330.19425.7791-0.64112.0635-0.243-1.13280.39731.11660.1761-0.711-0.05890.2810.06690.0552-0.0849-0.04530.4585-0.1296-0.123745.0216-53.852699.5931
34.1017-1.754-0.93884.77361.9462.6887-0.2392-0.6977-0.69220.78560.05690.78270.2991-0.08790.1822-0.0617-0.0257-0.00230.15210.21880.1787-5.73832.743888.2097
42.5080.5745-0.13935.6651-0.96641.28220.22380.2921-0.4043-1.4354-0.233-0.36490.13180.11230.00920.35710.1248-0.01390.0454-0.1696-0.08111.229210.726547.5136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 5471 - 518
2X-RAY DIFFRACTION2BB3 - 5471 - 518
3X-RAY DIFFRACTION3CC3 - 5471 - 518
4X-RAY DIFFRACTION4DD3 - 5471 - 518

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