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- PDB-1tlw: Tsx structure complexed with thymidine -

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Basic information

Entry
Database: PDB / ID: 1tlw
TitleTsx structure complexed with thymidine
ComponentsNucleoside-specific channel-forming protein tsx
KeywordsMEMBRANE PROTEIN / nucleoside transporter / BETA BARREL / thymidine
Function / homology
Function and homology information


nucleoside-specific channel forming porin activity / nucleoside transport / pore complex / monoatomic ion transport / cell outer membrane / symbiont entry into host cell
Similarity search - Function
Nucleoside-specific channel-forming protein, Tsx-like / Nucleoside-specific channel-forming protein Tsx / Nucleoside-specific channel-forming protein, Tsx-like / Nucleoside-specific channel-forming protein, Tsx-like superfamily / Nucleoside-specific channel-forming protein, Tsx / Outer membrane phospholipase (ompla); Chain C / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
THYMIDINE / Nucleoside-specific channel-forming protein Tsx
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsYe, J. / van den Berg, B.
CitationJournal: Embo J. / Year: 2004
Title: Crystal structure of the bacterial nucleoside transporter Tsx.
Authors: Ye, J. / Van Den Berg, B.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside-specific channel-forming protein tsx
B: Nucleoside-specific channel-forming protein tsx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5076
Polymers64,5382
Non-polymers9694
Water0
1
A: Nucleoside-specific channel-forming protein tsx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7543
Polymers32,2691
Non-polymers4842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside-specific channel-forming protein tsx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7543
Polymers32,2691
Non-polymers4842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.653, 149.653, 119.939
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Nucleoside-specific channel-forming protein tsx


Mass: 32269.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TSX, NUPA, B0411, Z0512, ECS0464, SF0348, S0356 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P0A927
#2: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2O5

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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: 6.2 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 286 K / Method: soaking the crystal with 10 mm thymidine / pH: 4.3
Details: PEG550 27-32%, sodium acetate 50 mM, glycerol 10%, pH 4.3, soaking the crystal with 10 mM thymidine, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 28482 / Num. obs: 27650 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Limit h max: 43 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 39 / Limit l min: 0 / Observed criterion F max: 255288.33 / Observed criterion F min: 0.32

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→29.34 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2072 7.5 %RANDOM
Rwork0.269 ---
all0.269 28481 --
obs0.297 25578 97.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 17.7464 Å2 / ksol: 0.288706 e/Å3
Displacement parametersBiso max: 165.07 Å2 / Biso mean: 62.29 Å2 / Biso min: 19.45 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å24.06 Å20 Å2
2---3.52 Å20 Å2
3---7.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.35 Å
Luzzati d res high-3.1
Refinement stepCycle: LAST / Resolution: 3.1→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 68 0 4194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg26.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.1-3.240.3292387.30.32230020.0213522324092
3.24-3.410.3242457.30.26531100.0213520335595.3
3.41-3.620.28927280.2531480.0183520342097.1
3.62-3.90.262667.70.23231830.0163530344997.7
3.9-4.30.3042356.70.26232510.023545348698.3
4.3-4.920.272627.40.24332590.0173556352199
4.92-6.180.2842888.10.25432760.0173597356499.1
6.18-29.340.3052667.40.28233490.0193706361597.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5Thy.top

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