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- PDB-6e8j: Crystal Structure of A Bacterial Homolog to Human Lysosomal Trans... -

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Basic information

Entry
Database: PDB / ID: 6e8j
TitleCrystal Structure of A Bacterial Homolog to Human Lysosomal Transporter, Spinster, in Inward-facing And Occupied Conformation
ComponentsMajor facilitator family transporter
KeywordsTRANSPORT PROTEIN / antiporter / Major facilitator superfamily / spinster homolog
Function / homologyProtein spinster-like / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / transmembrane transporter activity / membrane / Major facilitator family transporter
Function and homology information
Biological speciesHyphomonas neptunium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.091 Å
AuthorsZhou, F. / Yao, D. / Rao, B. / Zhang, L. / Cao, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1632132 China
National Natural Science Foundation of China (NSFC)31670849 China
National Basic Research Program of China (973 Program)2017YFC1001303 China
CitationJournal: Sci Bull (Beijing) / Year: 2019
Title: Crystal structure of a bacterial homolog to human lysosomal transporter, spinster
Authors: Zhou, F. / Yao, D. / Rao, B. / Zhang, L. / Nie, W. / Zou, Y. / Zhao, J., / Cao, Y.
History
DepositionJul 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _citation.journal_id_ISSN / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major facilitator family transporter


Theoretical massNumber of molelcules
Total (without water)54,2911
Polymers54,2911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.709, 89.419, 122.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Major facilitator family transporter / Spinster-like protein


Mass: 54291.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomonas neptunium (strain ATCC 15444) (bacteria)
Strain: ATCC 15444 / Gene: HNE_0949 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0C3L7

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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: 4.46 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 32.5%(v/v) PEG 400, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 18325 / % possible obs: 99.7 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 17.5
Reflection shellResolution: 3.09→3.28 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.091→44.71 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.18
RfactorNum. reflection% reflection
Rfree0.2976 3382 9.89 %
Rwork0.2572 --
obs0.2612 18325 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.091→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 0 0 3519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093622
X-RAY DIFFRACTIONf_angle_d1.1384943
X-RAY DIFFRACTIONf_dihedral_angle_d2.8262061
X-RAY DIFFRACTIONf_chiral_restr0.062565
X-RAY DIFFRACTIONf_plane_restr0.014611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0909-3.13510.41081250.39321168X-RAY DIFFRACTION91
3.1351-3.18190.41181500.35591313X-RAY DIFFRACTION100
3.1819-3.23160.37511430.35681283X-RAY DIFFRACTION100
3.2316-3.28450.35321430.30611297X-RAY DIFFRACTION100
3.2845-3.34110.34031300.28511271X-RAY DIFFRACTION100
3.3411-3.40190.3141350.26781292X-RAY DIFFRACTION100
3.4019-3.46730.30981410.26891273X-RAY DIFFRACTION100
3.4673-3.5380.32711450.25581311X-RAY DIFFRACTION100
3.538-3.61490.29431290.26661294X-RAY DIFFRACTION100
3.6149-3.6990.34921490.25081312X-RAY DIFFRACTION100
3.699-3.79140.25351330.23631261X-RAY DIFFRACTION100
3.7914-3.89390.27781450.21631319X-RAY DIFFRACTION100
3.8939-4.00840.30791430.23211246X-RAY DIFFRACTION99
4.0084-4.13770.26631420.23551276X-RAY DIFFRACTION100
4.1377-4.28550.30121500.23471293X-RAY DIFFRACTION100
4.2855-4.45690.30331410.23631294X-RAY DIFFRACTION100
4.4569-4.65950.26051510.22251287X-RAY DIFFRACTION100
4.6595-4.90490.22531440.20781294X-RAY DIFFRACTION100
4.9049-5.21180.28821420.21361287X-RAY DIFFRACTION100
5.2118-5.61350.29071480.2581266X-RAY DIFFRACTION100
5.6135-6.17710.35211400.26721285X-RAY DIFFRACTION100
6.1771-7.06790.27021340.26051295X-RAY DIFFRACTION100
7.0679-8.89330.22411350.22911311X-RAY DIFFRACTION100
8.8933-44.71420.36051440.32321278X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -26.0704 Å / Origin y: -2.802 Å / Origin z: 14.1661 Å
111213212223313233
T0.5439 Å2-0.032 Å20.0077 Å2-0.5206 Å2-0.0055 Å2--0.5509 Å2
L0.0387 °20.009 °20.0156 °2-0.0357 °2-0.0051 °2--0.0223 °2
S-0.0327 Å °0.0895 Å °-0.0265 Å °-0.1049 Å °0.0277 Å °-0.0082 Å °-0.008 Å °0.0317 Å °-0 Å °
Refinement TLS groupSelection details: all

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