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- PDB-5ul7: Structure and function of the divalent anion/Na+ symporter from V... -

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Basic information

Entry
Database: PDB / ID: 5ul7
TitleStructure and function of the divalent anion/Na+ symporter from Vibrio cholerae and a humanized variant
ComponentsTransporter, NadC familyTransport protein
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


succinate transmembrane transporter activity / membrane / identical protein binding
Similarity search - Function
Citrate transporter-like domain / Citrate transporter / Sodium/sulphate symporter, conserved site / Sodium:sulfate symporter family signature. / Solute carrier family 13
Similarity search - Domain/homology
SUCCINIC ACID / Transporter, NadC family
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLu, M.
CitationJournal: Nat Commun / Year: 2017
Title: Structure and function of the divalent anion/Na(+) symporter from Vibrio cholerae and a humanized variant.
Authors: Nie, R. / Stark, S. / Symersky, J. / Kaplan, R.S. / Lu, M.
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter, NadC family
B: Transporter, NadC family
C: Transporter, NadC family
D: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,80716
Polymers190,1514
Non-polymers65612
Water0
1
A: Transporter, NadC family
B: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4038
Polymers95,0752
Non-polymers3286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-37 kcal/mol
Surface area35480 Å2
MethodPISA
2
C: Transporter, NadC family
D: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4038
Polymers95,0752
Non-polymers3286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-37 kcal/mol
Surface area35470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.694, 101.918, 167.755
Angle α, β, γ (deg.)90.00, 98.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLNGLNAA18 - 4621 - 445
21LEULEUGLNGLNBB18 - 4621 - 445
31LEULEUGLNGLNCC18 - 4621 - 445
41LEULEUGLNGLNDD18 - 4621 - 445
12NANASINSINAE - G501 - 503
22NANASINSINBH - J501 - 503
32NANASINSINCK - M501 - 503
42NANASINSINDN - P501 - 503

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Components

#1: Protein
Transporter, NadC family / Transport protein


Mass: 47537.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KNE0
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4

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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: 4.74 Å3/Da / Density % sol: 74.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: PEG, Na+, etc. / PH range: 7 / Temp details: 293 K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 82858 / % possible obs: 99.9 % / Redundancy: 13 % / Net I/σ(I): 21

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.628 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27016 3988 5 %RANDOM
Rwork0.26045 ---
obs0.26085 75407 90.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.876 Å2
Baniso -1Baniso -2Baniso -3
1-11.87 Å20 Å211.12 Å2
2---11.12 Å2-0 Å2
3----2.38 Å2
Refinement stepCycle: 1 / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13348 0 40 0 13388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01913692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.96118668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16651776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96723.619420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.638152168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4121520
X-RAY DIFFRACTIONr_chiral_restr0.0710.22316
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219840
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.6668.687116
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.23213.0148888
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9719.1216576
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.02774.54622151
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3347 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A7.76
2B16.13
3C8.68
4D13.43
LS refinement shellResolution: 2.801→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 185 -
Rwork0.421 3768 -
obs--63.83 %

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