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- PDB-5ys3: 1.8 angstrom crystal structure of Succinate-Acetate Permease from... -

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Basic information

Entry
Database: PDB / ID: 5ys3
Title1.8 angstrom crystal structure of Succinate-Acetate Permease from Citrobacter koseri
ComponentsSuccinate-Acetate Permease
KeywordsTRANSPORT PROTEIN / organic anion channel / rectifying / unidirectional / dehydration
Function / homology
Function and homology information


acetate:proton symporter activity / succinate transmembrane transport / plasma membrane
Similarity search - Function
Acetate transporter GPR1/FUN34/SatP family / : / : / GPR1/FUN34/yaaH family / GPR1/FUN34/yaaH family signature.
Similarity search - Domain/homology
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / ACETATE ION / PALMITIC ACID / Acetate uptake transporter
Similarity search - Component
Biological speciesCitrobacter koseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.823 Å
AuthorsQiu, B. / Liao, J.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2017YFA0504800 China
National Science and Technology Major Project2017ZX09101005-003-003 China
National Key Scientific Instrument and Equipment Development Program2012YQ03026010 China
Joint Fund of the National Natural Science Foundation of China and the Israel Science Foundation Research Program8146114802 China
China Post-Doctoral Science Foundation2016M600344 China
CitationJournal: Cell Res. / Year: 2018
Title: Succinate-acetate permease from Citrobacter koseri is an anion channel that unidirectionally translocates acetate
Authors: Qiu, B. / Xia, B. / Zhou, Q. / Lu, Y. / He, M. / Hasegawa, K. / Ma, Z. / Zhang, F. / Gu, L. / Mao, Q. / Wang, F. / Zhao, S. / Gao, Z. / Liao, J.
History
DepositionNov 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinate-Acetate Permease
B: Succinate-Acetate Permease
C: Succinate-Acetate Permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,24838
Polymers61,4203
Non-polymers5,82835
Water3,135174
1
A: Succinate-Acetate Permease
B: Succinate-Acetate Permease
C: Succinate-Acetate Permease
hetero molecules

A: Succinate-Acetate Permease
B: Succinate-Acetate Permease
C: Succinate-Acetate Permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,49676
Polymers122,8396
Non-polymers11,65770
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area36320 Å2
ΔGint-247 kcal/mol
Surface area35700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.456, 79.456, 89.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein Succinate-Acetate Permease


Mass: 20473.240 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) (bacteria)
Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_03375 / Production host: Escherichia coli (E. coli) / References: UniProt: A8ALU5
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6.5 / Details: PEG 400, CaAc2, NaCl / PH range: 4.0-6.5 / Temp details: PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 51162 / % possible obs: 99.6 % / Redundancy: 6.9 % / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.7 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v1.0data reduction
XDSv1.0data reduction
HKL-2000v1.0data scaling
SHELXDv1.0phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.823→39.728 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 2303 4.75 %
Rwork0.1601 --
obs0.1619 48460 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.823→39.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 259 174 4591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084511
X-RAY DIFFRACTIONf_angle_d1.1296039
X-RAY DIFFRACTIONf_dihedral_angle_d14.1291532
X-RAY DIFFRACTIONf_chiral_restr0.046678
X-RAY DIFFRACTIONf_plane_restr0.006744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8231-1.86280.341310.29592764X-RAY DIFFRACTION94
1.8628-1.90610.27961520.24232867X-RAY DIFFRACTION99
1.9061-1.95380.25791330.21142871X-RAY DIFFRACTION99
1.9538-2.00660.26971540.2042895X-RAY DIFFRACTION98
2.0066-2.06560.25011350.19412886X-RAY DIFFRACTION98
2.0656-2.13230.24011560.17482831X-RAY DIFFRACTION97
2.1323-2.20850.2111460.16512803X-RAY DIFFRACTION96
2.2085-2.29690.22161370.1592903X-RAY DIFFRACTION100
2.2969-2.40150.21351350.14692959X-RAY DIFFRACTION100
2.4015-2.5280.20991320.14252896X-RAY DIFFRACTION99
2.528-2.68640.1671340.13632886X-RAY DIFFRACTION98
2.6864-2.89380.1781610.13322835X-RAY DIFFRACTION97
2.8938-3.18490.20831680.14762949X-RAY DIFFRACTION100
3.1849-3.64540.17821210.14252937X-RAY DIFFRACTION100
3.6454-4.59180.15261430.14482917X-RAY DIFFRACTION98
4.5918-39.73740.18621650.16832958X-RAY DIFFRACTION99

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