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- PDB-4n7x: The E254A mutant of the sodium bile acid symporter from Yersinia ... -

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Basic information

Entry
Database: PDB / ID: 4n7x
TitleThe E254A mutant of the sodium bile acid symporter from Yersinia frederiksenii
ComponentsTransporter, sodium/bile acid symporter family
KeywordsTRANSPORT PROTEIN / slc10 / sodium symport / bile acid / membrane protein / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homologyNa+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Up-down Bundle / Mainly Alpha / :
Function and homology information
Biological speciesYersinia frederiksenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsZhou, X. / Levin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nature / Year: 2013
Title: Structural basis of the alternating-access mechanism in a bile acid transporter.
Authors: Zhou, X. / Levin, E.J. / Pan, Y. / McCoy, J.G. / Sharma, R. / Kloss, B. / Bruni, R. / Quick, M. / Zhou, M.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: Transporter, sodium/bile acid symporter family


Theoretical massNumber of molelcules
Total (without water)33,3081
Polymers33,3081
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.162, 73.859, 85.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transporter, sodium/bile acid symporter family


Mass: 33307.770 Da / Num. of mol.: 1 / Mutation: E254A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia frederiksenii (bacteria) / Gene: yfred0001_28600 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4ST46
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 8.5
Details: 39% PEG 400, 100 mM Tris-HCL, 100 mM KCl, 20 mM MnCl2, 1-oleoyl-rac-glycerol, pH 8.5, Lipid Cubic Phase, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99991 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99991 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12188 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 40.64 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.615 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.547.70.4164940.404180.5
2.54-2.598.30.3665310.37187.2
2.59-2.649.40.3695610.367195.4
2.64-2.6910.20.3286150.438197.9
2.69-2.7511.60.3475950.427199
2.75-2.8212.80.3236020.3941100
2.82-2.8913.60.3286130.4121100
2.89-2.9614.20.2616200.4371100
2.96-3.0514.40.2376180.4591100
3.05-3.1514.60.1875980.4951100
3.15-3.2614.50.1616160.5371100
3.26-3.3914.40.1346290.581100
3.39-3.5514.40.1156040.6151100
3.55-3.7314.40.0866270.6521100
3.73-3.9714.30.0636100.7491100
3.97-4.2714.20.0546231.0521100
4.27-4.714.10.0576360.9871100
4.7-5.3813.90.0626460.7721100
5.38-6.7813.40.066510.8551100
6.78-5012.80.0326990.787199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.758 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.829 / SU ML: 0.18 / σ(F): 1.37 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 609 5.02 %
Rwork0.2093 11533 -
obs0.2113 12142 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.98 Å2 / Biso mean: 42.3333 Å2 / Biso min: 21.34 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 0 14 2305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032348
X-RAY DIFFRACTIONf_angle_d0.793207
X-RAY DIFFRACTIONf_chiral_restr0.054399
X-RAY DIFFRACTIONf_plane_restr0.005384
X-RAY DIFFRACTIONf_dihedral_angle_d10.473809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.75160.24821460.17152646279292
2.7516-3.14970.24711600.192728843044100
3.1497-3.96790.25641540.205429223076100
3.9679-45.7660.24481490.225730813230100

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