[English] 日本語
Yorodumi
- PDB-6lgy: Crystal structure of a cysteine-pair mutant (P10C-S291C) of a bac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lgy
TitleCrystal structure of a cysteine-pair mutant (P10C-S291C) of a bacterial bile acid transporter in an inward-facing state complexed with glycine and sodium
ComponentsTransporter, sodium/bile acid symporter family
KeywordsTRANSPORT PROTEIN / Bile acid transporter / ASBT / NTCP / SLC10
Function / homologyBile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / GLYCINE / Ketopantoate/pantoate/pantothenate transporter PanS
Function and homology information
Biological speciesYersinia frederiksenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.247 Å
AuthorsWang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770783 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Substrate binding in the bile acid transporter ASBT Yf from Yersinia frederiksenii.
Authors: Wang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X.
History
DepositionDec 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,2806
Polymers33,3881
Non-polymers8925
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.469, 185.578, 75.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 33387.898 Da / Num. of mol.: 1 / Mutation: P10C, S291C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia frederiksenii (bacteria) / Gene: NCTC11470_02445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A380PV03

-
Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-A6L / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / monoolein


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 8.5
Details: 0.05 M Na2SO4, 0.05 M Li2SO4, 0.05 M Tris-HCl pH 8.5, 35% PEG 400, 0.8 mM CHAPSO, with 100 mM glycine pH 7.3 soaking

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.247→38.066 Å / Num. obs: 15449 / % possible obs: 98.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 36.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.057 / Rrim(I) all: 0.128 / Net I/σ(I): 10.4 / Num. measured all: 78877
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.247-2.2855.30.91941027760.4490.4481.0291.999.1
6.09-38.06650.03340228090.9990.0160.03731.593.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LGV

6lgv


Resolution: 2.247→34.8 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 733 4.75 %
Rwork0.2073 14695 -
obs0.209 15428 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.99 Å2 / Biso mean: 45.0129 Å2 / Biso min: 28.22 Å2
Refinement stepCycle: final / Resolution: 2.247→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 60 47 2443
Biso mean--69.96 50.1 -
Num. residues----311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.247-2.420.3021600.2187288699
2.42-2.66350.25041290.2158294299
2.6635-3.04870.24471590.2057289599
3.0487-3.84020.24021520.2012296499
3.8402-34.80.22791330.2072300896
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)
11.7348-0.0409-0.33367.7316-1.9942.0852-0.1842-0.26070.46481.0840.48610.2149-0.3293-0.5108-0.20510.5175-0.03490.05840.5241-0.08950.434-13.3109-19.95613.5707
21.8411-0.42130.60812.2005-0.66511.77330.0662-0.2273-0.2456-0.0094-0.06050.45790.2892-0.3737-0.03840.2745-0.03640.02690.3685-0.03350.4044-17.5892-30.84471.0781
31.81160.6979-0.1721.3470.05211.1184-0.0876-0.0221-0.0995-0.01770.1145-0.0528-0.014-0.0302-0.0420.37450.02730.02070.3579-0.01950.33320.5279-23.2924-5.0174
43.6165-2.1877-0.25992.85980.27170.97150.22950.35210.4085-0.3798-0.2273-0.02870.0635-0.1772-0.02890.4840.0196-0.01410.43290.01820.3985-10.4748-29.9207-12.8164
51.2442-2.1821.77384.3526-2.89362.96910.1647-0.15860.2605-0.3817-0.3133-0.05470.49740.0790.10360.347-0.04160.03430.4203-0.03380.4712-18.3413-21.04661.8542
61.01090.24990.39791.3006-0.00870.76720.00370.0277-0.05330.11830.056-0.13960.0269-0.0448-0.01160.36720.0270.01140.3805-0.00130.33191.9673-26.27092.9419
71.09350.26430.71273.62770.31471.70680.0303-0.14430.1446-0.1043-0.1643-0.1222-0.2773-0.15560.15750.42610.00840.03490.37750.00720.3806-0.5313-18.82668.8728
8222222-1.32992.0422-0.48392.68946.9753-10.5641-4.190913.4792-5.66320.4654-0.0449-0.14790.9847-0.41480.6325-8.853-26.7041.7969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 22 )A-4 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 48 )A23 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 144 )A49 - 144
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 178 )A145 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 208 )A179 - 208
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 273 )A209 - 273
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 306 )A274 - 306
8X-RAY DIFFRACTION8chain 'A' and (resid 401 through 401 )A401

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more