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- PDB-5ys8: 2.8 angstrom crystal structure of Succinate-Acetate Permease from... -

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Basic information

Entry
Database: PDB / ID: 5ys8
Title2.8 angstrom crystal structure of Succinate-Acetate Permease from Citrobacter koseri
ComponentsSuccinate-Acetate Permease
KeywordsTRANSPORT PROTEIN / organic anion channel / rectifying / unidirectional / dehydration
Function / homologyAcetate transporter GPR1/FUN34/SatP family / GPR1/FUN34/yaaH family / GPR1/FUN34/yaaH family signature. / membrane / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / ACETATE ION / Acetate uptake transporter
Function and homology information
Biological speciesCitrobacter koseri ATCC BAA-895 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 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 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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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)62,59910
Polymers61,4203
Non-polymers1,1807
Water1267
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)125,19920
Polymers122,8396
Non-polymers2,35914
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area24730 Å2
ΔGint-275 kcal/mol
Surface area34570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.874, 79.874, 88.501
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 ATCC BAA-895 (bacteria)
Strain: ATCC BAA-895 / Gene: CKO_03375 / Production host: Escherichia coli (E. coli) / References: UniProt: A8ALU5
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6.5 / Details: PEG 400, CaAc2, NaCl / PH range: 4.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13837 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 1 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.75 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.38 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
XDSv1.0data reduction
XDSv1.0data scaling
PHENIXv1.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YS3

5ys3


Resolution: 2.798→47.61 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3025 1378 10 %
Rwork0.2449 --
obs0.2505 13784 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.798→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 78 7 4173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014267
X-RAY DIFFRACTIONf_angle_d0.3535769
X-RAY DIFFRACTIONf_dihedral_angle_d11.0682373
X-RAY DIFFRACTIONf_chiral_restr0.032661
X-RAY DIFFRACTIONf_plane_restr0.003710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7978-2.89780.41951360.33451224X-RAY DIFFRACTION99
2.8978-3.01380.33971410.30121225X-RAY DIFFRACTION100
3.0138-3.15090.38181350.29131250X-RAY DIFFRACTION100
3.1509-3.3170.39981420.30921244X-RAY DIFFRACTION100
3.317-3.52470.36791360.30721223X-RAY DIFFRACTION100
3.5247-3.79680.2921440.26441230X-RAY DIFFRACTION99
3.7968-4.17870.33011380.25041236X-RAY DIFFRACTION100
4.1787-4.78280.27481490.22571235X-RAY DIFFRACTION100
4.7828-6.0240.26661330.22191251X-RAY DIFFRACTION99
6.024-47.61720.22071240.18091288X-RAY DIFFRACTION100

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