[English] 日本語
Yorodumi
- PDB-2reo: Crystal structure of human sulfotransferase 1C3 (Sult1C3) in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2reo
TitleCrystal structure of human sulfotransferase 1C3 (Sult1C3) in complex with PAP
ComponentsPutative sulfotransferase 1C3
KeywordsTRANSFERASE / sulfotransferase / SULFATE CONJUGATION / PAP / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / aryl sulfotransferase / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfur compound metabolic process / xenobiotic metabolic process ...alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / aryl sulfotransferase / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfur compound metabolic process / xenobiotic metabolic process / cholesterol metabolic process / lipid metabolic process / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase 1C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.651 Å
AuthorsTempel, W. / Pan, P. / Dong, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human sulfotransferase 1C3 (Sult1C3) in complex with PAP.
Authors: Pan, P. / Tempel, W. / Dong, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionSep 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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: Putative sulfotransferase 1C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3942
Polymers35,9671
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.230, 93.230, 146.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsAuthors state that the biological unit of this protein is unknown.

-
Components

#1: Protein Putative sulfotransferase 1C3


Mass: 35966.605 Da / Num. of mol.: 1 / Mutation: C40A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1C3 / Plasmid: pET28a-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL
References: UniProt: Q6IMI6, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Diammonium tartrate, 0.1M MES, 18% PEG 2000, 5% Ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2007 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 11518 / % possible obs: 99.8 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.061 / Χ2: 1.053 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.7414.10.97811021.068198.7
2.74-2.8518.70.62611070.8751100
2.85-2.9820.20.42411350.9031100
2.98-3.1420.40.25611180.9181100
3.14-3.3420.20.16311420.9491100
3.34-3.620.10.09511321.0361100
3.6-3.9619.80.06411451.1131100
3.96-4.5319.60.04711571.1781100
4.53-5.718.90.04511861.4651100
5.7-4017.30.02812941.024199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.65 Å39.32 Å
Translation2.65 Å39.32 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H8K

2h8k


Resolution: 2.651→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.215 / SU B: 22.45 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.429 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B factors are residuals from TLS refinement. Programs coot, molprobity have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 548 4.787 %RANDOM
Rwork0.226 ---
all0.228 11447 --
obs0.228 11447 99.686 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.116 Å2
Baniso -1Baniso -2Baniso -3
1--1.251 Å2-0.626 Å20 Å2
2---1.251 Å20 Å2
3---1.877 Å2
Refinement stepCycle: LAST / Resolution: 2.651→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 27 0 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221870
X-RAY DIFFRACTIONr_bond_other_d0.0020.021222
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9592548
X-RAY DIFFRACTIONr_angle_other_deg0.84632988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85424.44481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.04153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022027
X-RAY DIFFRACTIONr_gen_planes_other00.02381
X-RAY DIFFRACTIONr_nbd_refined0.2230.2417
X-RAY DIFFRACTIONr_nbd_other0.1820.21182
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2921
X-RAY DIFFRACTIONr_nbtor_other0.0850.2875
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.22
X-RAY DIFFRACTIONr_mcbond_it1.8221225
X-RAY DIFFRACTIONr_mcbond_other0.4012437
X-RAY DIFFRACTIONr_mcangle_it2.66531805
X-RAY DIFFRACTIONr_scbond_it1.7752875
X-RAY DIFFRACTIONr_scangle_it2.3953743
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.651-2.7190.316410.35376481898.411
2.719-2.7930.36410.27775379799.624
2.793-2.8740.297300.23974177399.741
2.874-2.9610.319390.22871575799.604
2.961-3.0570.277440.23869574099.865
3.057-3.1630.289380.23668572499.862
3.163-3.2810.288250.22264967599.852
3.281-3.4140.235390.224636675100
3.414-3.5630.225310.21760864099.844
3.563-3.7350.281200.20659661999.515
3.735-3.9330.252280.20456059099.661
3.933-4.1670.24160.193544560100
4.167-4.4490.316240.19514538100
4.449-4.7970.222250.182467492100
4.797-5.2410.271220.204448470100
5.241-5.8380.427270.22839842699.765
5.838-6.6990.237200.256367387100
6.699-8.1040.294120.275322334100
8.104-11.0640.27130.191259272100
11.064-300.278130.36417819697.449
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)
15.49250.60431.08853.9399-0.63465.5393-0.02930.10270.1454-0.04290.2205-0.06790.78970.0969-0.19120.07990.017-0.0394-0.21970.05790.00299.2575-27.19151.7852
212.033-8.329-0.13845.77360.23672.3815-0.05130.17840.2973-0.1020.1561-0.85540.26490.5949-0.10480.1233-0.0121-0.0171-0.1868-0.0034-0.030415.5388-25.26245.1664
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A42 - 30443 - 305
22B4011

+
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