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- PDB-2xq2: Structure of the K294A mutant of vSGLT -

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Basic information

Entry
Database: PDB / ID: 2xq2
TitleStructure of the K294A mutant of vSGLT
Components(SODIUM/GLUCOSE COTRANSPORTER) x 2
KeywordsTRANSPORT PROTEIN / INVERTED REPEATS / LEUT-FOLD / GALACTOSE / TRANSPORTER
Function / homology
Function and homology information


D-glucose:sodium symporter activity / 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
DI(HYDROXYETHYL)ETHER / Sodium/glucose cotransporter
Similarity search - Component
Biological speciesVIBRIO PARAHAEMOLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsWatanabe, A. / Choe, S. / Chaptal, V. / Rosenberg, J.M. / Wright, E.M. / Grabe, M. / Abramson, J.
CitationJournal: Nature / Year: 2010
Title: The Mechanism of Sodium and Substrate Release from the Binding Pocket of Vsglt
Authors: Watanabe, A. / Choe, S. / Chaptal, V. / Rosenberg, J.M. / Wright, E.M. / Grabe, M. / Abramson, J.
History
DepositionSep 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2Dec 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: SODIUM/GLUCOSE COTRANSPORTER
B: SODIUM/GLUCOSE COTRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,3205
Polymers127,0012
Non-polymers3183
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-15.7 kcal/mol
Surface area41910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.300, 112.680, 238.770
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: (-0.949, -0.30143, -0.09237), (-0.30426, 0.79897, 0.51871), (-0.08255, 0.52037, -0.84994)
Vector: -16.54956, 6.77973, -32.86922)

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Components

#1: Protein SODIUM/GLUCOSE COTRANSPORTER / VSGLT / NA(+)/GLUCOSE SYMPORTER


Mass: 64142.344 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO PARAHAEMOLYTICUS (bacteria) / Plasmid: PBAD18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: P96169
#2: Protein SODIUM/GLUCOSE COTRANSPORTER / VSGLT / NA(+)/GLUCOSE SYMPORTER


Mass: 62859.148 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO PARAHAEMOLYTICUS (bacteria) / Plasmid: PBAD18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: P96169
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 294 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 411 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LYS 294 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 411 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 423 TO CYS ENGINEERED RESIDUE IN CHAIN B, LYS 294 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 411 TO ALA ENGINEERED RESIDUE IN CHAIN B, ALA 423 TO CYS
Sequence detailsK294A IS AN ENGINEERED MUTATION. C411A AND A423C HAVE ALSO BEEN INTRODUCED TO GIVE HIGHER ...K294A IS AN ENGINEERED MUTATION. C411A AND A423C HAVE ALSO BEEN INTRODUCED TO GIVE HIGHER EXPRESSION. THE PROTEIN WITH THESE TWO MUTATIONS BEHAVES LIKE WILD-TYPE. UNK RESIDUES B 12-27 REPRESENT SECTION OF CHAIN B STRUCTURE WITH NO ASSIGNED SEQUENCE. ACTUAL SEQUENCE OF CHAIN B IS SUPPOSED TO BE IDENTICAL TO CHAIN A, FOR RESIDUES 1-50, SEQUENCE ASSIGNMENT COULD NOT BE DONE IN THE ELECTRON DENSITY DUE TO UNKNOWN REGISTER.

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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: 4.3 Å3/Da / Density % sol: 71.4 %
Description: 5 DATASETS WERE COLLECTED ON 4 CRYSTALS AND MERGED
Crystal growpH: 6.5 / Details: 0.1M MES PH 6.5, 4% MPD, 9-13% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→68 Å / Num. obs: 62421 / % possible obs: 98.9 % / Observed criterion σ(I): -0.5 / Redundancy: 7.5 % / Biso Wilson estimate: 65.22 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.4 / % possible all: 94.8

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DH4

3dh4


Resolution: 2.73→68.01 Å / Cor.coef. Fo:Fc: 0.8345 / Cor.coef. Fo:Fc free: 0.8639 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ELECTRON DENSITY QUALITY WAS BETTER FOR CHAIN A. CHAIN B WAS BUILT LARGELY WITH CHAIN A AS A MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 2690 5.07 %RANDOM
Rwork0.2509 ---
obs0.252 53054 --
Displacement parametersBiso mean: 112.01 Å2
Baniso -1Baniso -2Baniso -3
1-5.914 Å20 Å20 Å2
2---10.0441 Å20 Å2
3---4.1301 Å2
Refine analyzeLuzzati coordinate error obs: 0.604 Å
Refinement stepCycle: LAST / Resolution: 2.73→68.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8064 0 21 5 8090
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018219HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1611197HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2594SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1201HARMONIC5
X-RAY DIFFRACTIONt_it8201HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion21.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1143SEMIHARMONIC5
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_contact10446SEMIHARMONIC4
LS refinement shellResolution: 2.73→2.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3008 41 5.83 %
Rwork0.231 662 -
all0.2347 703 -
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)
11.1265-0.153-0.78472.09420.67756.1163-0.02440.31910.2487-0.5442-0.1337-0.1469-0.3091-0.22330.15810.30330.0572-0.034-0.3040.06570.0575-1.6965-36.4554-61.944
20.42680.7132-1.76020.64741.16370.99320.0039-0.0394-0.01110.0062-0.04770.0589-0.01050.03560.0438-0.11940.152-0.008-0.2563-0.07390.2285-7.8592-24.2407-40.729
30-0.713-1.18593.5612-1.0110.07470.0106-0.15150.052-0.01420.03070.0229-0.07390.0014-0.04120.304-0.066-0.152-0.30040.11550.22421.6953-18.2678-42.4709
41.32920.07610.0725.03490.44353.5498-0.03360.20970.0395-0.5442-0.0605-0.04010.54420.2180.09410.3040.1141-0.0285-0.30360.04190.07331.8908-41.9267-56.6007
51.36770.6315-0.82075.9188-0.76663.2232-0.0977-0.0720.1232-0.405-0.3172-0.5442-0.1130.54420.415-0.29980.152-0.0684-0.3040.08080.068511.5872-35.2304-48.4237
60.27640.6125-0.82860.424-1.142600.00640.02790.01560.0491-0.0125-0.00160.01120.0380.0061-0.30340.0989-0.0340.12960.09160.02015.7787-37.5328-29.6229
71.2195-2.839-0.68638.31552.91043.25890.0396-0.38890.35330.048-0.0860.2286-0.20850.25370.04640.3040.0264-0.152-0.2568-0.10290.05032.7066-22.254-24.9116
82.01380.23511.27174.8842-1.27373.51050.0565-0.0009-0.1965-0.1640.06790.54420.2571-0.5311-0.1244-0.0509-0.0119-0.0714-0.304-0.10.2925-17.632-41.4935-49.4698
91.1365-1.24452.43790.368-1.25820.53530.02280.0726-0.0401-0.06250.03840.03170.0292-0.0053-0.06120.12210.085-0.1503-0.16920.08810.0706-12.8125-27.3577-68.5656
100.05130.26641.8268.3155-2.84756.71280.0793-0.5442-0.3059-0.0958-0.06760.31780.0236-0.0011-0.01170.3040.152-0.0207-0.20010.152-0.3041.8061-53.8813-0.1481
110.04921.28720.23160.10440.71080.30410.0045-0.0587-0.00460.05110.00970.04870.01740.046-0.01430.2898-0.0294-0.1177-0.1373-0.1416-0.16741.8837-31.4724-10.1802
1201.172-2.91040.14621.80880.5574-0.0052-0.05930.03320.03460.0146-0.0277-0.0581-0.0206-0.00930.29220.1130.15-0.1536-0.152-0.0545-8.8451-30.4959-6.4321
130.06710.8040.32472.9025-2.3654.85450.1271-0.5442-0.45510.5442-0.40430.33520.54420.3420.27720.3040.1520.152-0.3040.152-0.304-0.3645-56.735-7.1714
141.5256-0.3869-1.35412.1870.17143.4124-0.0032-0.5442-0.17080.5242-0.14680.29110.4684-0.54310.150.304-0.03140.152-0.3040.0221-0.304-12.9392-49.6288-12.0126
1500.17230.513600.789700.0073-0.0135-0.00460.0182-0.00630.046-0.0058-0.0415-0.0010.12420.1130.0886-0.2752-0.0547-0.1888-7.993-40.4691-27.6962
1600.8672-1.22494.81052.1491.6895-0.0568-0.04380.17840.17020.03750.0118-0.0117-0.13510.01930.3040.1520.152-0.304-0.152-0.0908-10.1277-24.8782-23.5162
172.458-2.91042.91043.38030.8867.44790.0301-0.3452-0.22570.0219-0.0544-0.3117-0.19610.46160.02430.28130.1309-0.152-0.29950.1519-0.270617.1809-46.2544-10.9783
180-1.70270.61740.0043-1.00350.61750.0097-0.00350.0251-0.006-0.01560.05490.03310.02240.00590.14710.0787-0.10060.03390.0965-0.21679.7824-47.738712.2016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A10 - A97 )
2X-RAY DIFFRACTION2(A98 - A107 )
3X-RAY DIFFRACTION3(A108 - A117 )
4X-RAY DIFFRACTION4(A118 - A338 )
5X-RAY DIFFRACTION5(A339 - A486 )
6X-RAY DIFFRACTION6(A487 - A491 )
7X-RAY DIFFRACTION7(A492 - A516 )
8X-RAY DIFFRACTION8(A517 - A561 )
9X-RAY DIFFRACTION9(A562 - A573 )
10X-RAY DIFFRACTION10(B12 - B97 )
11X-RAY DIFFRACTION11(B98 - B107 )
12X-RAY DIFFRACTION12(B108 - B117 )
13X-RAY DIFFRACTION13(B118 - B338 )
14X-RAY DIFFRACTION14(B339 - B486 )
15X-RAY DIFFRACTION15(B487 - B491 )
16X-RAY DIFFRACTION16(B492 - B516 )
17X-RAY DIFFRACTION17(B517 - B561 )
18X-RAY DIFFRACTION18(B562 - B573 )

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