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- PDB-6okz: Structure of VcINDY bound to Fumarate -

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Basic information

Entry
Database: PDB / ID: 6okz
TitleStructure of VcINDY bound to Fumarate
ComponentsTransporter, NadC familyTransport protein
Keywordsmembrane protein / transport protein / Complex / Transporter
Function / homology
Function and homology information


succinate transmembrane transporter activity / membrane / identical protein binding
Similarity search - Function
Citrate transporter-like domain / Citrate transporter / Sodium:sulfate symporter transmembrane region / Sodium/sulphate symporter, conserved site / Sodium:sulfate symporter family signature. / Solute carrier family 13
Similarity search - Domain/homology
FUMARIC ACID / Transporter, NadC family
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.292 Å
AuthorsSauer, D.B. / Marden, J. / Wang, D.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM121994 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01-NS108151 United States
CitationJournal: Biorxiv / Year: 2022
Title: Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter
Authors: Klinz-Thompson, C.D. / Redondo, M.L. / Mulligan, C. / Sauer, D.B. / Marden, J.J. / Song, J. / Tajkhorshid, E. / Hunt, J.F. / Stokes, D.L. / Mindell, J.A. / Wang, D.N. / Gonzalez, R.L.
History
DepositionApr 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)193,02313
Polymers192,6294
Non-polymers3939
Water0
1
C: Transporter, NadC family
D: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5237
Polymers96,3152
Non-polymers2085
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-35 kcal/mol
Surface area34050 Å2
MethodPISA
2
A: Transporter, NadC family
B: Transporter, NadC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5006
Polymers96,3152
Non-polymers1854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-34 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.795, 102.063, 171.173
Angle α, β, γ (deg.)90.00, 98.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transporter, NadC family / Transport protein


Mass: 48157.359 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.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4

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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: 74.05 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 37.5% PEG 300, 100mM Sodium Acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.29→50 Å / Num. obs: 51510 / % possible obs: 93.9 % / Redundancy: 6.6 % / Net I/σ(I): 10.1
Reflection shellResolution: 3.29→3.35 Å / Num. unique obs: 1913

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Processing

Software
NameVersionClassification
PHENIX(1.15.1_3469: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UL9

5ul9


Resolution: 3.292→47.903 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2857 1991 3.88 %
Rwork0.2469 --
obs0.2483 51327 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.292→47.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13097 0 23 0 13120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213420
X-RAY DIFFRACTIONf_angle_d0.45418302
X-RAY DIFFRACTIONf_dihedral_angle_d2.2157739
X-RAY DIFFRACTIONf_chiral_restr0.0332278
X-RAY DIFFRACTIONf_plane_restr0.0052215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2918-3.37410.3951060.36162619X-RAY DIFFRACTION70
3.3741-3.46530.39651170.3462892X-RAY DIFFRACTION78
3.4653-3.56720.33211300.32343208X-RAY DIFFRACTION85
3.5672-3.68230.39011380.31533436X-RAY DIFFRACTION91
3.6823-3.81390.3681430.30123523X-RAY DIFFRACTION94
3.8139-3.96650.31861460.2693620X-RAY DIFFRACTION96
3.9665-4.14690.27931500.25073678X-RAY DIFFRACTION98
4.1469-4.36540.29271510.22643758X-RAY DIFFRACTION100
4.3654-4.63870.23971520.20383777X-RAY DIFFRACTION100
4.6387-4.99660.25561500.19683721X-RAY DIFFRACTION100
4.9966-5.49870.25161500.21293758X-RAY DIFFRACTION99
5.4987-6.29290.29821520.23963785X-RAY DIFFRACTION100
6.2929-7.92260.24831520.24473775X-RAY DIFFRACTION99
7.9226-47.90810.27671540.24733786X-RAY DIFFRACTION98

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