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Basic information

Entry
Database: PDB / ID: 5xat
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 ANION / Citrate/sodium symporter
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.76 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_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)187,62211
Polymers186,6944
Non-polymers9297
Water724
1
A: Citrate-sodium symporter
D: Citrate-sodium symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8746
Polymers93,3472
Non-polymers5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-60 kcal/mol
Surface area30560 Å2
MethodPISA
2
B: Citrate-sodium symporter
C: Citrate-sodium symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7485
Polymers93,3472
Non-polymers4013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-61 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.668, 91.874, 96.320
Angle α, β, γ (deg.)86.10, 82.22, 69.66
Int Tables number1
Space group name H-MP1
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
11LYSLYSGLYGLYAA22 - 44312 - 433
21LYSLYSGLYGLYBB22 - 44312 - 433
12PHEPHEMETMETAA21 - 44511 - 435
22PHEPHEMETMETCC21 - 44511 - 435
13LYSLYSMETMETAA22 - 44512 - 435
23LYSLYSMETMETDD22 - 44512 - 435
14LYSLYSGLYGLYBB22 - 44312 - 433
24LYSLYSGLYGLYCC22 - 44312 - 433
15LYSLYSGLYGLYBB22 - 44312 - 433
25LYSLYSGLYGLYDD22 - 44312 - 433
16LYSLYSMETMETCC22 - 44512 - 435
26LYSLYSMETMETDD22 - 44512 - 435

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: Escherichia coli (E. coli) / References: UniProt: P31602
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#4: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 3.79 Å3/Da / Density % sol: 67.53 %
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: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.76→95.41 Å / Num. obs: 26874 / % possible obs: 99.2 % / Redundancy: 1.9 % / Net I/σ(I): 21.2
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 1.9 % / % possible all: 98.6

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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: 3.76→95.41 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.917 / SU B: 74.878 / SU ML: 0.916 / Cross valid method: THROUGHOUT / ESU R Free: 0.809 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29815 1401 5.2 %RANDOM
Rwork0.26748 ---
obs0.26908 25473 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 238.985 Å2
Baniso -1Baniso -2Baniso -3
1--14.59 Å24.45 Å2-4.59 Å2
2--2.51 Å2-2.87 Å2
3---13.15 Å2
Refinement stepCycle: 1 / Resolution: 3.76→95.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12271 0 62 4 12337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912569
X-RAY DIFFRACTIONr_bond_other_d0.0080.0212787
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.97717056
X-RAY DIFFRACTIONr_angle_other_deg1.609329226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.46351633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02622.791387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.869152078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2051546
X-RAY DIFFRACTIONr_chiral_restr0.1560.22080
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213901
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022793
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_it13.81623.8146556
X-RAY DIFFRACTIONr_mcbond_other13.81723.8136555
X-RAY DIFFRACTIONr_mcangle_it22.10635.7258181
X-RAY DIFFRACTIONr_mcangle_other22.10435.7268182
X-RAY DIFFRACTIONr_scbond_it12.20724.36013
X-RAY DIFFRACTIONr_scbond_other12.20724.36013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other20.25236.2338875
X-RAY DIFFRACTIONr_long_range_B_refined34.49256598
X-RAY DIFFRACTIONr_long_range_B_other34.49256598
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)
11A528340.05
12B528340.05
21A522240.07
22C522240.07
31A450860.15
32D450860.15
41B522420.06
42C522420.06
51B447300.15
52D447300.15
61C448720.15
62D448720.15
LS refinement shellResolution: 3.764→3.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 71 -
Rwork0.47 1483 -
obs--74.25 %

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