[English] 日本語
Yorodumi
- PDB-4eec: Crystal Structure of the glycopeptide antibiotic sulfotransferase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eec
TitleCrystal Structure of the glycopeptide antibiotic sulfotransferase StaL complexed with A3P and desulfo-A47934.
Components
  • StaL
  • desulfo-A47934
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / sulfotransferase / glycopeptide aglycone complex / Glycopeptide antibiotic sulfotransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


desulfo-A47934 sulfotransferase / sulfation / sulfotransferase activity / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #460 / Sulfotransferase domain / Sulfotransferase domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
desulfo-A47934 / ADENOSINE-3'-5'-DIPHOSPHATE / Desulfo-A47934 sulfotransferase
Similarity search - Component
Biological speciesStreptomyces toyocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShi, R. / Cygler, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of sulfonation of the glycopeptide antibiotic scaffold by the sulfotransferase StaL
Authors: Shi, R. / Munger, C. / Kalan, L. / Sulea, T. / Wright, G.D. / Cygler, M.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: StaL
B: StaL
C: desulfo-A47934
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5514
Polymers65,1243
Non-polymers4271
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.442, 82.583, 123.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein StaL


Mass: 31941.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Strain: NRRL 15009 / Gene: stal / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KLM3
#2: Protein/peptide desulfo-A47934


Type: Glycopeptide / Class: Antibiotic / Mass: 1241.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: stal gene knock out / Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Production host: Streptomyces toyocaensis (bacteria) / References: desulfo-A47934
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 295 K / Method: microbatch, under oil / pH: 8.5
Details: 0.5M LiCl, 0.1M Tris pH 8.5, 28% PEG-6K, microbatch, under oil, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 15536 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.076 / Χ2: 1.681 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.755.80.5967671.1131100
2.75-2.85.90.4937771.1691100
2.8-2.8560.4867621.2231100
2.85-2.916.20.4387481.2051100
2.91-2.976.10.397601.2891100
2.97-3.046.10.3167601.3551100
3.04-3.126.10.2867621.3661100
3.12-3.26.10.2127651.4781100
3.2-3.36.10.1747721.4551100
3.3-3.46.10.1237521.4291100
3.4-3.5260.1087801.4631100
3.52-3.6660.0827621.6641100
3.66-3.8360.0747771.8661100
3.83-4.0360.0657702.2061100
4.03-4.295.90.0627772.532199.9
4.29-4.625.80.0577922.5741100
4.62-5.085.90.0517782.3551100
5.08-5.815.80.0468052.0011100
5.81-7.325.70.048021.9681100
7.32-505.20.0298681.912197.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OVF

2ovf


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 1 / SU B: 35.68 / SU ML: 0.333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 773 5 %RANDOM
Rwork0.2227 ---
obs0.2252 15434 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 130.16 Å2 / Biso mean: 65.292 Å2 / Biso min: 28.14 Å2
Baniso -1Baniso -2Baniso -3
1-8.07 Å20 Å20 Å2
2---0.52 Å20 Å2
3----7.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 27 10 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213997
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9835430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7465490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85122.982171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.31415578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1811531
X-RAY DIFFRACTIONr_chiral_restr0.1010.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213078
X-RAY DIFFRACTIONr_mcbond_it0.721.52491
X-RAY DIFFRACTIONr_mcangle_it1.32223943
X-RAY DIFFRACTIONr_scbond_it1.93731506
X-RAY DIFFRACTIONr_scangle_it3.2144.51487
LS refinement shellResolution: 2.7→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 62 -
Rwork0.324 1039 -
all-1101 -
obs--98.3 %
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)
11.06180.13050.21531.93360.05971.93170.0524-0.05160.00430.0148-0.07560.17920.0346-0.02070.02320.0237-0.0145-0.00910.0199-0.00530.0255-21.6183-0.13081.1934
21.07220.26360.04841.6829-0.30542.5006-0.0931-0.00820.066-0.08940.06490.1101-0.26-0.1570.02820.08020.0099-0.03870.0745-0.01790.0322-15.676211.465734.8015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 269
2X-RAY DIFFRACTION2B2 - 269

+
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