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- PDB-4tkr: Native-SAD phasing for ThiT from Listeria monocytogenes serovar. -

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Basic information

Entry
Database: PDB / ID: 4tkr
TitleNative-SAD phasing for ThiT from Listeria monocytogenes serovar.
ComponentsThiamine transporter thia
KeywordsMEMBRANE PROTEIN / transporter / native-SAD phasing / multiple crystals / low energy / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information


thiamine transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Thiamine transporter ThiT / Thiamine transporter protein (Thia_YuaJ) / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Energy-coupled thiamine transporter ThiT / Energy-coupled thiamine transporter ThiT
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.0023 Å
AuthorsGuo, Y. / Liu, Q. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095315 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107462 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Multi-crystal native SAD analysis at 6 keV.
Authors: Liu, Q. / Guo, Y. / Chang, Y. / Cai, Z. / Assur, Z. / Mancia, F. / Greene, M.I. / Hendrickson, W.A.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Oct 22, 2014Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag ..._entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiamine transporter thia
B: Thiamine transporter thia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,39519
Polymers48,1592
Non-polymers5,23617
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-22 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.647, 95.647, 125.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thiamine transporter thia


Mass: 24079.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: M637_10125, M638_09860, M640_06115, M641_06335, M643_01630, M644_08810, M645_06650
Production host: Escherichia coli (E. coli) / References: UniProt: S5L6I0, UniProt: A0A0B8R2U7*PLUS
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Sugar
ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M tri-sodium citrate dihydrate, pH 5.6, 30% w/v polyethylene glycol (PEG) 4000, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 2.07366 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07366 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 13687 / % possible obs: 99.8 % / Redundancy: 140.2 % / Net I/σ(I): 39.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 3.0023→39.315 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1267 4.97 %
Rwork0.1978 --
obs0.1997 25496 99.79 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.0023→39.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 342 0 3172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023255
X-RAY DIFFRACTIONf_angle_d0.664400
X-RAY DIFFRACTIONf_dihedral_angle_d12.3621082
X-RAY DIFFRACTIONf_chiral_restr0.041527
X-RAY DIFFRACTIONf_plane_restr0.002476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0023-3.12250.31821440.25142651X-RAY DIFFRACTION99
3.1225-3.26450.30251300.23392716X-RAY DIFFRACTION100
3.2645-3.43650.23181450.19092688X-RAY DIFFRACTION100
3.4365-3.65170.31241340.19472703X-RAY DIFFRACTION100
3.6517-3.93340.18891350.18872682X-RAY DIFFRACTION100
3.9334-4.32880.20351480.1782693X-RAY DIFFRACTION100
4.3288-4.95410.22821500.17452704X-RAY DIFFRACTION100
4.9541-6.23760.19551430.19242686X-RAY DIFFRACTION100
6.2376-39.31870.24691380.22632706X-RAY DIFFRACTION100
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)
13.00470.5336-0.11651.38290.36510.76760.00450.2783-0.2068-0.07340.01190.01950.13120.0549-0.03590.25040.037-0.0030.587-0.01320.383211.512433.871636.3927
22.4213-0.8975-0.1171.7632-0.31251.5477-0.0038-0.108-0.11830.07920.02920.0650.1301-0.1664-0.02370.2252-0.0311-0.00530.52610.07450.3758-10.357335.825149.0674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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