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- PDB-1tly: Tsx structure -

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Basic information

Entry
Database: PDB / ID: 1tly
TitleTsx structure
ComponentsNucleoside-specific channel-forming protein tsx
KeywordsMEMBRANE PROTEIN / nucleoside transporter / BETA BARREL
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
Nucleoside-specific channel-forming protein Tsx
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.01 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 1.3Dec 17, 2014Group: Data collection
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)64,5382
Polymers64,5382
Non-polymers00
Water00
1
A: Nucleoside-specific channel-forming protein tsx


Theoretical massNumber of molelcules
Total (without water)32,2691
Polymers32,2691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside-specific channel-forming protein tsx


Theoretical massNumber of molelcules
Total (without water)32,2691
Polymers32,2691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.778, 149.778, 120.888
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

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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: vapor diffusion, hanging drop / pH: 4.3
Details: PEG550 27-32%, sodium acetate 50 mM, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97882 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97882 Å / Relative weight: 1
ReflectionResolution: 3.01→49.03 Å / Num. all: 60045 / Observed criterion σ(F): 0 / Limit h max: 43 / Limit h min: -24 / Limit k max: 49 / Limit k min: -24 / Limit l max: 40 / Limit l min: -40 / Observed criterion F max: 216141.02 / 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: 3.01→29.76 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 4307 7.4 %RANDOM
Rwork0.262 ---
all0.262 60097 --
obs0.288 58328 97.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 50.9609 Å2 / ksol: 0.359054 e/Å3
Displacement parametersBiso max: 172.53 Å2 / Biso mean: 67.38 Å2 / Biso min: 20.38 Å2
Baniso -1Baniso -2Baniso -3
1--7.37 Å22.03 Å20 Å2
2---7.37 Å20 Å2
3---14.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Luzzati d res high-3.01
Refinement stepCycle: LAST / Resolution: 3.01→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 0 0 4126
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg26.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.72
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 (%)
3.01-3.150.364787.10.34462990.0167501677790.3
3.15-3.310.3395597.90.29765360.0147540709594.1
3.31-3.520.2854856.60.24568320.0137500731797.6
3.52-3.790.265767.80.24168310.0117521740798.5
3.79-4.170.2795907.90.25568670.0117547745798.8
4.17-4.770.2535527.40.23568920.0117489744499.4
4.77-6.010.2775357.10.25969620.0127536749799.5
6.01-29.760.3255327.30.368020.0147508733497.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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