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Entry
Database: PDB / ID: 5xas
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 / homology2-hydroxycarboxylate transporter / 2-hydroxycarboxylate transporter, Proteobacteria/Firmicutes / 2-hydroxycarboxylate transporter family / citrate metabolic process / organic anion transmembrane transporter activity / symporter activity / plasma membrane / CITRATE ANION / Citrate-sodium symporter
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 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_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.pdbx_dist_value / _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
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)94,0637
Polymers93,3472
Non-polymers7175
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-71 kcal/mol
Surface area29500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.705, 83.340, 81.060
Angle α, β, γ (deg.)97.14, 100.16, 94.59
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 22 - 446 / Label seq-ID: 12 - 436

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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / 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
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: 3.37 Å3/Da / Density % sol: 67.07 %
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: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.47→82.24 Å / Num. obs: 16295 / % possible obs: 97 % / Redundancy: 1.9 % / Net I/σ(I): 14
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.5 / % possible all: 94.8

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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: 3.47→82.24 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.846 / SU B: 117.268 / SU ML: 0.703 / Cross valid method: THROUGHOUT / ESU R Free: 0.668 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29503 849 5.2 %RANDOM
Rwork0.24579 ---
obs0.24823 15446 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 148.455 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å24.12 Å20.75 Å2
2---10.13 Å21.26 Å2
3---10.72 Å2
Refinement stepCycle: 1 / Resolution: 3.47→82.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6106 0 48 4 6158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196272
X-RAY DIFFRACTIONr_bond_other_d0.0080.026386
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9828514
X-RAY DIFFRACTIONr_angle_other_deg1.468314598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3635812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69622.775191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.787151033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.111522
X-RAY DIFFRACTIONr_chiral_restr0.1740.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026919
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021387
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_it4.87611.0943260
X-RAY DIFFRACTIONr_mcbond_other4.87511.0923259
X-RAY DIFFRACTIONr_mcangle_it8.02316.6324068
X-RAY DIFFRACTIONr_mcangle_other8.02216.6334069
X-RAY DIFFRACTIONr_scbond_it4.31411.5063012
X-RAY DIFFRACTIONr_scbond_other4.30311.5023010
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.36317.1044446
X-RAY DIFFRACTIONr_long_range_B_refined14.93529096
X-RAY DIFFRACTIONr_long_range_B_other14.93529097
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 45086 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.465→3.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 49 -
Rwork0.415 863 -
obs--74.21 %
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)
12.5044-0.11610.49764.8015-1.56141.94080.02610.58230.305-0.42290.0035-0.0419-0.07540.2317-0.02970.1098-0.07370.06490.2325-0.00350.0942-37.9281-51.861130.5575
21.3728-0.0918-0.67174.2422-0.86492.26530.0123-0.509-0.420.6528-0.0180.0640.2440.05710.00570.3067-0.1114-0.01040.34410.07850.225-39.4026-82.052956.5269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 446
2X-RAY DIFFRACTION2B16 - 446

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