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Basic information

Entry
Database: PDB / ID: 5x9r
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 / : / 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
beta-D-glucopyranose / CITRATE ANION / Citrate/sodium symporter
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.98 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 Foundation (NRF)NRF-2014R1A1A3050966 Korea, Republic Of
National Research Foundation (NRF)NRF-2015M2A2A4A03044653 Korea, Republic Of
National Research Foundation (NRF)NRF-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 8, 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.name / _chem_comp.type ..._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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0856
Polymers93,3472
Non-polymers7394
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-61 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.998, 93.998, 172.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 21 - 444 / Label seq-ID: 11 - 434

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 46673.430 Da / Num. of mol.: 2 / 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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 71.13 %
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, 5mM Sodium Citrate
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: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.98→94 Å / Num. obs: 12743 / % possible obs: 99.2 % / Redundancy: 6.8 % / Net I/σ(I): 30.2
Reflection shellResolution: 4→4.1 Å / % possible obs: 99.9 % / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.9

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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: 3.98→94 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.898 / SU B: 143.199 / SU ML: 0.785 / Cross valid method: THROUGHOUT / ESU R Free: 0.941 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3233 596 4.7 %RANDOM
Rwork0.27259 ---
obs0.27473 12147 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 269.517 Å2
Baniso -1Baniso -2Baniso -3
1-4.9 Å2-0 Å2-0 Å2
2--4.9 Å2-0 Å2
3----9.81 Å2
Refinement stepCycle: 1 / Resolution: 3.98→94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6183 0 50 0 6233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196351
X-RAY DIFFRACTIONr_bond_other_d0.0040.026441
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.988623
X-RAY DIFFRACTIONr_angle_other_deg1.054314724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7565821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72322.755196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.144151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.451523
X-RAY DIFFRACTIONr_chiral_restr0.1620.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027006
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021413
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_it5.7619.5983296
X-RAY DIFFRACTIONr_mcbond_other5.76119.5983295
X-RAY DIFFRACTIONr_mcangle_it9.53729.3954113
X-RAY DIFFRACTIONr_mcangle_other9.53529.3944114
X-RAY DIFFRACTIONr_scbond_it5.17320.1933055
X-RAY DIFFRACTIONr_scbond_other5.16720.1943055
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.00630.0634511
X-RAY DIFFRACTIONr_long_range_B_refined17.97728255
X-RAY DIFFRACTIONr_long_range_B_other17.97628253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 51914 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.981→4.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 44 -
Rwork0.551 891 -
obs--96.59 %
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)
15.0414-1.7509-0.12025.6535-0.68394.10190.08260.0783-0.5858-0.18250.0225-0.08111.49630.6314-0.10510.7660.0065-0.04340.3513-0.05480.091629.314637.3034-14.4139
24.9933-2.48170.32875.0615-0.43853.2520.04570.18720.4623-0.3024-0.03120.8081-1.0173-1.2805-0.01450.59940.1414-0.08390.83910.03520.34594.428367.7709-17.1833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 445
2X-RAY DIFFRACTION2B21 - 444

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