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Basic information

Entry
Database: PDB / ID: 5xar
TitleStructural insights into the elevator-like mechanism of the sodium/citrate symporter CitS
ComponentsCitrate-sodium symporter
KeywordsTRANSPORT PROTEIN / CitS / citrate transporter / sodium/citrate symporter / 2-HCT
Function / homology
Function and homology information


citrate metabolic process / symporter activity / organic anion transmembrane transporter activity / sodium ion transport / metal ion binding / plasma membrane
Similarity search - Function
2-hydroxycarboxylate transporter / 2-hydroxycarboxylate transporter, Proteobacteria/Firmicutes / 2-hydroxycarboxylate transporter family
Similarity search - Domain/homology
Citrate/sodium symporter
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsJin, M.S. / Kim, J.W. / Kim, S. / Kim, S. / Lee, H. / Lee, J.-O.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research FoundationNRF-2014R1A1A3050966 Korea, Republic Of
National Research FoundationNRF-2015M2A2A4A03044653 Korea, Republic Of
National Research FoundationNRF-2014R1A2A1A10050436 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2017
Title: Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS
Authors: Kim, J.W. / Kim, S. / Kim, S. / Lee, H. / Lee, J.O. / Jin, M.S.
History
DepositionMar 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: 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 / pdbx_initial_refinement_model / 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.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: Citrate-sodium symporter
B: Citrate-sodium symporter
C: Citrate-sodium symporter
D: Citrate-sodium symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,37010
Polymers186,6944
Non-polymers6776
Water1448
1
A: Citrate-sodium symporter
B: Citrate-sodium symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9786
Polymers93,3472
Non-polymers6314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-60 kcal/mol
Surface area30120 Å2
MethodPISA
2
C: Citrate-sodium symporter
D: Citrate-sodium symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3934
Polymers93,3472
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-59 kcal/mol
Surface area30130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.367, 163.994, 93.670
Angle α, β, γ (deg.)90.00, 93.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUILEILEAA18 - 4468 - 436
21LEULEUILEILEBB18 - 4468 - 436
12LEULEUILEILEAA18 - 4468 - 436
22LEULEUILEILECC18 - 4468 - 436
13LEULEUILEILEAA18 - 4468 - 436
23LEULEUILEILEDD18 - 4468 - 436
14LEULEUILEILEBB18 - 4468 - 436
24LEULEUILEILECC18 - 4468 - 436
15SERSERMETMETBB16 - 4456 - 435
25SERSERMETMETDD16 - 4456 - 435
16LEULEUILEILECC18 - 4468 - 436
26LEULEUILEILEDD18 - 4468 - 436

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Citrate-sodium symporter / Citrate carrier protein / Citrate transporter


Mass: 46673.430 Da / Num. of mol.: 4 / Fragment: UNP residues 13-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: citS / Production host: Bacteria (eubacteria) / References: UniProt: P31602
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthor replaced the 7-PPATEK-12 amino acid region of KpCitS with a thrombin recognition sequence (LVPRGS)

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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: 3.44 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.0-6.5, 100-200 mM NaCl, 32-36% PEG400
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→93.49 Å / Num. obs: 30477 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 22.7
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A1S

5a1s


Resolution: 3.62→93.49 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.931 / SU B: 106.757 / SU ML: 0.623 / Cross valid method: THROUGHOUT / ESU R Free: 0.647 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26734 1433 4.7 %RANDOM
Rwork0.23459 ---
obs0.23614 29044 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 189.555 Å2
Baniso -1Baniso -2Baniso -3
1-10.85 Å20 Å29.36 Å2
2---11.48 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 3.62→93.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12355 0 44 8 12407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01912653
X-RAY DIFFRACTIONr_bond_other_d0.0080.0212917
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.97717172
X-RAY DIFFRACTIONr_angle_other_deg1.336329520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.65651642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3922.732388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.201152093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8591545
X-RAY DIFFRACTIONr_chiral_restr0.1060.22101
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213961
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022820
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_it8.79114.4146592
X-RAY DIFFRACTIONr_mcbond_other8.78814.4136591
X-RAY DIFFRACTIONr_mcangle_it13.78221.6348226
X-RAY DIFFRACTIONr_mcangle_other13.78121.6358227
X-RAY DIFFRACTIONr_scbond_it8.87814.9316061
X-RAY DIFFRACTIONr_scbond_other8.87714.936061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.29922.1768946
X-RAY DIFFRACTIONr_long_range_B_refined21.60857626
X-RAY DIFFRACTIONr_long_range_B_other21.60757626
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A521920.05
12B521920.05
21A533660.05
22C533660.05
31A526820.04
32D526820.04
41B519240.06
42C519240.06
51B518720.06
52D518720.06
61C523700.05
62D523700.05
LS refinement shellResolution: 3.625→3.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 109 -
Rwork0.396 1820 -
obs--85.62 %
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)
11.7973-0.11530.69112.99371.23233.16140.09720.1432-0.1657-0.8779-0.14640.5344-0.1828-0.26650.04920.27330.0374-0.14670.05940.01540.245-51.295828.1324-48.6228
21.7004-0.2258-0.10233.6114-0.90563.7788-0.0399-0.4046-0.22110.66160.1474-0.92510.30890.7225-0.10750.19220.1041-0.23590.3027-0.01340.4082-23.714224.2798-20.1519
33.59561.88261.76454.53450.46393.8561-0.0798-0.6030.28311.31950.2018-0.1176-0.2791-0.0858-0.1220.54320.1863-0.10880.2244-0.10650.075-39.890764.6792-8.3276
43.3101-0.45890.34023.2819-0.18652.1235-0.29390.46790.1422-0.5930.19051.1212-0.3787-0.36820.10350.2213-0.0353-0.25220.26710.02150.4581-64.197368.0326-39.6077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 446
2X-RAY DIFFRACTION2B16 - 446
3X-RAY DIFFRACTION3C18 - 446
4X-RAY DIFFRACTION4D13 - 446

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