[English] 日本語
Yorodumi
- PDB-30sh: Homotaurine ABC transporter substrate binding protein HtaA from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 30sh
TitleHomotaurine ABC transporter substrate binding protein HtaA from C. jiansuensis in complex with homotaurine
ComponentsTaurine ABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / substrate-binding protein / organosulfonate metabolism / SBP
Function / homologyalkanesulfonate transmembrane transport / Taurine ABC transporter, substrate-binding protein TauA / NMT1-like family / Solute-binding protein family 3/N-terminal domain of MltF / Bacterial periplasmic substrate-binding proteins / periplasmic space / 3-aminopropane-1-sulfonic acid / Taurine ABC transporter substrate-binding protein
Function and homology information
Biological speciesCaballeronia jiangsuensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBarber, H. / Jin, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: A Bacterial Pathway for Homotaurine Catabolism via Sulfopropanoate
Authors: Pallasdies, L. / Barber, H. / Lee, M. / Burchill, L. / Ho, H.N.N. / Stewart, A.W.E. / Nastasovici, A. / Sanne-Wander, H. / Rathnayake, D.T. / Hofferek, V. / Jebeli, L. / McDaniels, T.A. / ...Authors: Pallasdies, L. / Barber, H. / Lee, M. / Burchill, L. / Ho, H.N.N. / Stewart, A.W.E. / Nastasovici, A. / Sanne-Wander, H. / Rathnayake, D.T. / Hofferek, V. / Jebeli, L. / McDaniels, T.A. / McConville, M.J. / Field, R.A. / Pidot, S. / Scott, N.E. / Jin, Y. / Williams, S.J.
History
DepositionMay 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Taurine ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6933
Polymers33,4921
Non-polymers2012
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint2 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.02, 138.02, 45.939
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Taurine ABC transporter substrate-binding protein


Mass: 33491.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N terminal 6xHis tag with signal peptide deletion / Source: (gene. exp.) Caballeronia jiangsuensis (bacteria) / Gene: tauA, PQR08_32560 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0ABW9CX80
#2: Chemical ChemComp-A20 / 3-aminopropane-1-sulfonic acid


Mass: 139.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 44 % / Description: Needle-shaped
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 70mg/ml HtaA + 1:5 molar ratio Htau in 14% w/v PEG4000, 0.1 M sodium/potassium phosphate, pH 6.2, 6% v/v MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.8→69.01 Å / Num. obs: 30256 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.021 / Rrim(I) all: 0.05 / Χ2: 0.91 / Net I/σ(I): 19.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9-69.0111.30.022105.524310.0110.0251.0699.9
1.8-1.8410.81.994118230.5410.9452.2090.72100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.126)refinement
REFMAC5.8.0431 (refmacat 0.4.126)refinement
DIALSdata collection
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.875 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.174 / SU B: 7.727 / SU ML: 0.111 / Average fsc free: 0.9587 / Average fsc work: 0.9682 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.115 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1380 4.561 %RANDOM
Rwork0.1794 28874 --
all0.181 ---
obs-30254 99.993 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.979 Å20.489 Å2-0 Å2
2--0.979 Å20 Å2
3----3.175 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 12 128 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122435
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.7763309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.54757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31710397
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.55110100
X-RAY DIFFRACTIONr_chiral_restr0.0950.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021887
X-RAY DIFFRACTIONr_nbd_refined0.2050.21194
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.212
X-RAY DIFFRACTIONr_mcbond_it2.1793.2841249
X-RAY DIFFRACTIONr_mcangle_it2.7865.8931561
X-RAY DIFFRACTIONr_scbond_it2.9393.5361186
X-RAY DIFFRACTIONr_scangle_it4.1766.371745
X-RAY DIFFRACTIONr_lrange_it5.95237.4633845
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3171080.32921500.32822580.9390.9231000.333
1.847-1.8970.345780.29521000.29721780.9250.941000.296
1.897-1.9520.262960.27319910.27220870.9470.9491000.269
1.952-2.0120.2661000.25419800.25520800.9430.9581000.244
2.012-2.0780.31740.22419380.22720120.9430.9681000.208
2.078-2.1510.249980.20717960.20918940.9630.9731000.191
2.151-2.2320.2611010.19517780.19818790.9580.9771000.176
2.232-2.3220.222860.19416950.19517810.9690.9771000.179
2.322-2.4250.282870.18616290.1917160.9580.9791000.171
2.425-2.5430.257710.1915760.19216470.9580.9791000.175
2.543-2.680.201580.1815000.18115580.9750.9811000.169
2.68-2.8420.183810.17413940.17514750.9790.9821000.165
2.842-3.0370.231730.19113250.19313980.9660.9791000.183
3.037-3.2790.214520.20512310.20512830.9730.9751000.199
3.279-3.5890.25610.18611330.18911940.960.9811000.185
3.589-4.0090.192520.17310270.17410790.9760.9841000.175
4.009-4.6210.183340.1489070.159410.9820.9881000.154
4.621-5.6410.174300.1387790.1398090.9880.991000.144
5.641-7.8990.224220.1656080.1676310.9780.98599.84150.169
7.899-39.8750.13180.1383360.1373540.990.9881000.148
Refinement TLS params.Method: refined / Origin x: -26.8815 Å / Origin y: -13.345 Å / Origin z: -15.4149 Å
111213212223313233
T0.0414 Å20.0241 Å2-0.0153 Å2-0.0253 Å2-0.0183 Å2--0.1327 Å2
L3.3251 °2-0.3662 °20.3145 °2-1.0405 °2-0.2445 °2--2.0164 °2
S-0.0724 Å °-0.0079 Å °-0.315 Å °0.0047 Å °0.0302 Å °-0.1744 Å °0.1467 Å °0.1901 Å °0.0422 Å °
Refinement TLS groupSelection: ALL

+
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