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- PDB-4n7w: Crystal Structure of the sodium bile acid symporter from Yersinia... -

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Basic information

Entry
Database: PDB / ID: 4n7w
TitleCrystal Structure 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 / CITRIC ACID / Chem-MPG / :
Function and homology information
Biological speciesYersinia frederiksenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.951 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 1.2Jun 8, 2016Group: Atomic model
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,5446
Polymers65,4462
Non-polymers1,0974
Water2,648147
1
A: Transporter, sodium/bile acid symporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2723
Polymers32,7231
Non-polymers5492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transporter, sodium/bile acid symporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2723
Polymers32,7231
Non-polymers5492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-16 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.406, 46.223, 70.357
Angle α, β, γ (deg.)90.000, 100.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 32723.092 Da / Num. of mol.: 2
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: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#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


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 5.5
Details: 30% PEG 400, 100 mM sodium citrate, 100 mM NaCl, 3% (w/v) D-trehalose, 1-oleoyl-rac-glycerol, pH 5.5, 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: 0.99999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 43734 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.42 Å2 / Rmerge(I) obs: 0.076 / Χ2: 0.986 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.983.50.58621650.8031100
1.98-2.023.50.48121930.791199.2
2.02-2.063.60.41721500.8291100
2.06-2.13.50.36221840.938199.5
2.1-2.153.60.29621430.9951100
2.15-2.23.50.24122211.061100
2.2-2.253.60.22421251.118199.8
2.25-2.313.50.19622041.119199.9
2.31-2.383.60.16921601.1111100
2.38-2.463.50.14321901.2451100
2.46-2.543.50.13522141.1021100
2.54-2.653.60.11321501.137199.9
2.65-2.773.60.121971.0611100
2.77-2.913.60.09422070.9591100
2.91-3.13.60.08421930.9351100
3.1-3.333.60.07622010.9571100
3.33-3.673.60.07221990.912199.9
3.67-4.23.60.06122370.839199.9
4.2-5.293.40.0521190.895195.7
5.29-503.60.04722820.911198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.951→30.492 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8528 / SU ML: 0.17 / σ(F): 1.36 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 2219 5.08 %
Rwork0.1857 41499 -
obs0.1876 43718 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.5 Å2 / Biso mean: 33.7489 Å2 / Biso min: 13.04 Å2
Refinement stepCycle: LAST / Resolution: 1.951→30.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4575 0 76 147 4798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074761
X-RAY DIFFRACTIONf_angle_d1.096486
X-RAY DIFFRACTIONf_chiral_restr0.073803
X-RAY DIFFRACTIONf_plane_restr0.006777
X-RAY DIFFRACTIONf_dihedral_angle_d14.0951680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.951-1.99350.25211410.21192471261296
1.9935-2.03980.24271430.19642522266599
2.0398-2.09080.23761250.191326122737100
2.0908-2.14730.23671370.186525742711100
2.1473-2.21050.22191300.178726332763100
2.2105-2.28180.21551570.174125722729100
2.2818-2.36340.23271230.162825682691100
2.3634-2.45790.23861510.164626022753100
2.4579-2.56970.21241330.17226312764100
2.5697-2.70520.22581200.166826322752100
2.7052-2.87450.21461330.166425792712100
2.8745-3.09630.21371500.180526122762100
3.0963-3.40750.21141540.178725852739100
3.4075-3.89970.20521440.191426392783100
3.8997-4.90990.23631280.20142560268897
4.9099-30.49550.22781500.1972707285799
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)
11.9055-1.5168-1.00151.25010.66151.25950.0217-0.44190.65390.02220.2427-0.4564-0.20890.4653-0.20280.2838-0.0410.01070.2523-0.09650.3861-30.5515-8.332131.6694
22.5759-0.74150.25110.7239-0.27720.9336-0.0244-0.06770.10540.04420.0577-0.0481-0.10980.0894-0.0390.1898-0.01730.03920.123-0.04540.1456-30.3191-18.984328.2798
34.01820.18431.09140.9377-0.57333.84620.16550.2796-0.57930.16060.1132-0.33790.47720.1854-0.23650.35960.0482-0.0190.1493-0.09720.3524-28.1817-40.3815-12.8378
42.47960.7824-0.35731.26020.33621.67420.0963-0.364-0.04410.1411-0.041-0.05870.1460.2157-0.05550.25450.030.00840.2113-0.02630.1205-25.9139-24.58440.1194
51.85910.69860.53690.88180.1160.45010.03540.0532-0.22140.10090.0585-0.13280.11020.1624-0.09090.30130.03920.00890.2164-0.05120.1653-21.1783-30.8282-6.5036
64.28290.2287-1.22190.8761-0.28321.78980.0759-0.0368-0.14090.1019-0.0643-0.07940.13410.3388-0.03940.28880.0066-0.00810.2498-0.01940.136-22.5275-26.9788-10.7596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 60 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 307 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 48 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 49 through 164 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 165 through 259 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 260 through 306 )B0

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