[English] 日本語
Yorodumi
- PDB-7d1x: Crystal structure of 7-alpha-hydroxyl bile acid sulfotransferase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d1x
TitleCrystal structure of 7-alpha-hydroxyl bile acid sulfotransferase (Sult2a8)
ComponentsSulfotransferase
KeywordsTRANSFERASE / Bile acid / Sulfotransferase / Sult2a8 / 7-hydroxyl
Function / homology
Function and homology information


glycochenodeoxycholate sulfotransferase / bile acid catabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / sulfation / sulfotransferase activity / lipid catabolic process / cytosol / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / CHOLIC ACID / Sulfotransferase 2A8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAu, W.N.S. / Wang, K.
Citation
Journal: To be published
Title: Crystal structure of sulfotransferase Sult2A8 reveals the distinct mode of substrate binding for sulfonation at 7-hydroxyl group
Authors: Wang, K. / Chan, Y.C. / Lee, S.S.T. / Au, S.W.N.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Identification and characterization of a novel PPAR alpha-regulated and 7-alpha-hydroxyl bile acid-preferring cytosolic sulfotransferase mL-STL (Sult2a8)
Authors: Feng, L. / Yuen, Y.L. / Xu, J. / Liu, X. / Chan, Y.C. / Wang, K. / Fong, W.P. / Cheung, W.T. / Lee, S.S.T.
History
DepositionSep 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfotransferase
B: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4726
Polymers66,8012
Non-polymers1,6724
Water1,51384
1
A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2363
Polymers33,4001
Non-polymers8362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area13960 Å2
MethodPISA
2
B: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2363
Polymers33,4001
Non-polymers8362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.870, 93.870, 71.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-641-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 21 or resid 23...
d_2ens_1(chain "B" and (resid 6 through 21 or resid 23...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUALAA1 - 16
d_12ens_1ILEASPA18 - 29
d_13ens_1ASPASNA31 - 67
d_14ens_1ARGTYRA69 - 79
d_15ens_1ILESERA81 - 84
d_16ens_1LEUPROA90 - 101
d_17ens_1SERASNA103 - 130
d_18ens_1GLULEUA137 - 149
d_19ens_1GLYARGA151 - 221
d_110ens_1ILEILEA226
d_111ens_1PHEPHEA231 - 257
d_112ens_1GLUPHEA259 - 264
d_113ens_1CHDA3PB
d_21ens_1LEUALAC3 - 18
d_22ens_1ILEASPC20 - 31
d_23ens_1ASPASNC33 - 69
d_24ens_1ARGTYRC71 - 81
d_25ens_1ILESERC83 - 86
d_26ens_1LEUPROC88 - 99
d_27ens_1SERLEUC101 - 141
d_28ens_1GLYARGC143 - 213
d_29ens_1ILEILEC215
d_210ens_1PHEPHEC218 - 244
d_211ens_1GLUPHEC246 - 251
d_212ens_1CHDA3PD

NCS oper: (Code: givenMatrix: (-0.00969508060556, 0.999942141646, -0.00466034040359), (0.999952922324, 0.0096931187093, -0.000443380120896), (-0.000398181234895, -0.0046644196116, -0.999989042261) ...NCS oper: (Code: given
Matrix: (-0.00969508060556, 0.999942141646, -0.00466034040359), (0.999952922324, 0.0096931187093, -0.000443380120896), (-0.000398181234895, -0.0046644196116, -0.999989042261)
Vector: -47.5604217049, 46.6109153273, -35.1556341275)

-
Components

#1: Protein Sulfotransferase


Mass: 33400.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult2a8, 2810007J24Rik / Production host: Escherichia coli (E. coli)
References: UniProt: Q8BGL3, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: MES, PEG3350, MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→29.68 Å / Num. obs: 21605 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3135

-
Processing

Software
NameVersionClassification
PHENIXdev_3922refinement
CrystalCleardev_3922data collection
Cootmodel building
SCALEPACKdata scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F3Y

3f3y


Resolution: 2.5→29.68 Å / Cross valid method: FREE R-VALUE / σ(F): 4.4 / Phase error: 29.7074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2715 1084 5.02 %
Rwork0.2385 20508 -
obs0.2467 21592 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 112 84 4512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344553
X-RAY DIFFRACTIONf_angle_d0.72096187
X-RAY DIFFRACTIONf_chiral_restr0.0467673
X-RAY DIFFRACTIONf_plane_restr0.0061784
X-RAY DIFFRACTIONf_dihedral_angle_d11.718657
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.66852281149 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.33191290.35332551X-RAY DIFFRACTION95.19
2.61-2.750.35811370.3562561X-RAY DIFFRACTION94.92
2.75-2.920.37271330.32722519X-RAY DIFFRACTION94.98
2.92-3.150.3971350.31782563X-RAY DIFFRACTION95
3.15-3.470.291370.2642565X-RAY DIFFRACTION94.93
3.47-3.960.2961320.23212569X-RAY DIFFRACTION95.08
3.97-4.990.21171370.19572564X-RAY DIFFRACTION94.93
4.99-29.680.24371440.20782616X-RAY DIFFRACTION94.51
Refinement TLS params.Method: refined / Origin x: -31.8201183811 Å / Origin y: 15.8113362577 Å / Origin z: -18.1823145926 Å
111213212223313233
T0.556156248035 Å20.184628543091 Å20.0144227862669 Å2-0.342585597422 Å2-0.0156220195375 Å2--0.354838560336 Å2
L0.832372030045 °2-0.593371456203 °20.711320894914 °2-0.776902181305 °2-0.693561477678 °2--0.716173110479 °2
S-0.0137039458317 Å °0.022509967324 Å °-0.164447922175 Å °-0.065691164915 Å °0.0457922409068 Å °0.0251515924342 Å °0.120317650278 Å °0.122951526671 Å °-0.0340837519397 Å °
Refinement TLS groupSelection details: 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