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- PDB-5edl: Crystal structure of an S-component of ECF transporter -

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Basic information

Entry
Database: PDB / ID: 5edl
TitleCrystal structure of an S-component of ECF transporter
ComponentsPutative HMP/thiamine permease protein YkoE
KeywordsTRANSPORT PROTEIN / membrane transport protein
Function / homologyABC-type thiamin-related transport system, permease component 1, predicted / ABC-type cobalt transport system, permease component / membrane => GO:0016020 / plasma membrane / Chem-MPG / Chem-VIB / Putative HMP/thiamine permease protein YkoE
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsJosts, I. / Tidow, H.
CitationJournal: Cell Chem Biol / Year: 2016
Title: Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate.
Authors: Josts, I. / Almeida Hernandez, Y. / Andreeva, A. / Tidow, H.
History
DepositionOct 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _chem_comp.pdbx_synonyms ..._atom_site.occupancy / _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: Putative HMP/thiamine permease protein YkoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9604
Polymers20,9811
Non-polymers9783
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint6 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.713, 70.713, 196.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

21A-373-

HOH

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Components

#1: Protein Putative HMP/thiamine permease protein YkoE


Mass: 20981.166 Da / Num. of mol.: 1 / Fragment: UNP residues 3-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ykoE, BSU13230 / Production host: Escherichia coli (E. coli) / References: UniProt: O34738
#2: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1 / Thiamine


Mass: 265.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N4OS / Comment: medication*YM
#3: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 291 K / Method: lipidic cubic phase
Details: PEG1000, disodium hydrogen phosphate, citric acid, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→49.21 Å / Num. obs: 18753 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→44.579 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 962 5.13 %
Rwork0.1954 17785 -
obs0.1965 18747 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.58 Å2 / Biso mean: 33.5986 Å2 / Biso min: 17.01 Å2
Refinement stepCycle: final / Resolution: 1.95→44.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 91 74 1641
Biso mean--56.91 41.4 -
Num. residues----197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071564
X-RAY DIFFRACTIONf_angle_d0.9162109
X-RAY DIFFRACTIONf_chiral_restr0.036247
X-RAY DIFFRACTIONf_plane_restr0.004249
X-RAY DIFFRACTIONf_dihedral_angle_d12.674558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9503-2.05310.34541400.26624922632
2.0531-2.18180.24581290.213524812610
2.1818-2.35020.19481400.183624992639
2.3502-2.58670.20581400.160724992639
2.5867-2.96090.19121270.161125432670
2.9609-3.73020.20491430.187325652708
3.7302-44.59030.21741430.209327062849
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)
14.65860.6479-3.88141.7114-1.6917.56780.17710.13660.46770.06580.0127-0.0068-0.463-0.3914-0.35530.26190.0482-0.03280.2766-0.02950.32514.238524.542866.5156
24.5956-1.0219-3.84731.23191.42583.5291-0.0080.20660.131-0.134-0.0332-0.10160.0619-0.2305-0.0620.2726-0.0085-0.00740.26030.01130.269912.258821.042367.4979
32.8769-0.55111.07273.1034-0.94172.37970.15240.1988-0.019-0.2279-0.06480.08320.2805-0.2133-0.05230.2336-0.00460.03320.2943-0.03210.25763.291515.67767.3299
44.33714.26212.99454.59084.1197.1247-0.0101-0.61110.27450.3556-0.0006-0.19470.38720.51490.13880.32440.0642-0.00630.2623-0.01560.2459.752912.068184.9152
51.2286-0.7456-1.27332.7211.18153.66320.00760.02060.061-0.0948-0.0752-0.1003-0.06980.19550.05830.24540.0086-0.01820.27790.00840.297916.712916.725167.0187
66.3054.0979-5.12714.5232-5.80478.4470.4219-0.62340.60251.402-0.18851.6938-0.8997-0.649-0.06190.59790.1180.0410.4295-0.08560.49510.607328.928985.4921
75.31933.5863.75622.47522.6532.87970.3931-0.6048-0.4251.3567-0.0662-0.33590.9322-0.178-0.47440.65960.0368-0.02240.5212-0.08050.423210.01930.414696.7622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 37 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 60 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 105 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 112 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 174 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 180 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 181 through 199 )A0

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