[English] 日本語
Yorodumi
- PDB-9kf2: Crystal structure of Streptomyces sp. sulfotransferase Cpz8 in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kf2
TitleCrystal structure of Streptomyces sp. sulfotransferase Cpz8 in complex with PAP, involved in Caprazamycin synthesis
ComponentsSulfotransferase family protein
KeywordsBIOSYNTHETIC PROTEIN / sulfotransferase
Function / homologySulfotransferase, S. mansonii-type / Sulfotransferase domain / transferase activity / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase family protein
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsIwamoto, Y. / Watanabe, M. / Suzuki, K. / Teramoto, T. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K09353 Japan
CitationJournal: To Be Published
Title: Crystal structure of Streptomyces sp. sulfotransferase Cpz8 involved in Caprazamycin Synthesis
Authors: Iwamoto, Y. / Watanabe, M. / Kawano, K. / Suzuki, K. / Yazaki, M. / Arisawa, M. / Nishimoto, E. / Igarashi, M. / Teramoto, T. / Kakuta, Y.
History
DepositionNov 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0366
Polymers24,2321
Non-polymers8045
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.983, 44.161, 101.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sulfotransferase family protein


Mass: 24232.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: G3M58_47930 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6G3X8Q2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 1.81 Å3/Da / Density % sol: 32.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 23058 / % possible obs: 85.4 % / Redundancy: 5.4 % / CC1/2: 0.99 / Net I/σ(I): 10.5
Reflection shellResolution: 1.55→1.59 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 520 / CC1/2: 0.71

-
Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9KF1

9kf1


Resolution: 1.55→40.48 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 16.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1758 2000 8.67 %
Rwork0.1383 --
obs0.1416 23058 85.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 22 271 2033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061959
X-RAY DIFFRACTIONf_angle_d0.972684
X-RAY DIFFRACTIONf_dihedral_angle_d14.267749
X-RAY DIFFRACTIONf_chiral_restr0.054275
X-RAY DIFFRACTIONf_plane_restr0.012351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3815490.3319516X-RAY DIFFRACTION30
1.59-1.630.331750.2337795X-RAY DIFFRACTION46
1.63-1.680.2513990.17691040X-RAY DIFFRACTION61
1.68-1.730.17981250.14781311X-RAY DIFFRACTION76
1.73-1.80.19431450.14511533X-RAY DIFFRACTION89
1.8-1.870.18261620.1391702X-RAY DIFFRACTION98
1.87-1.950.19181630.13941705X-RAY DIFFRACTION100
1.95-2.050.18841650.13011751X-RAY DIFFRACTION100
2.05-2.180.15661640.12291732X-RAY DIFFRACTION100
2.18-2.350.17871690.12381764X-RAY DIFFRACTION100
2.35-2.590.15261650.12541747X-RAY DIFFRACTION100
2.59-2.960.16241690.12791777X-RAY DIFFRACTION100
2.96-3.730.14441700.12461794X-RAY DIFFRACTION100
3.73-40.480.18161800.1521891X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.1923 Å / Origin y: 17.8733 Å / Origin z: 62.299 Å
111213212223313233
T0.1508 Å2-0.0077 Å20.0024 Å2-0.1515 Å2-0.0072 Å2--0.1266 Å2
L1.0534 °20.056 °2-0.0874 °2-0.9612 °2-0.1629 °2--0.4768 °2
S-0.0034 Å °0.0212 Å °-0.0297 Å °-0.0282 Å °-0.0001 Å °-0.0209 Å °0.0416 Å °0.014 Å °0.0043 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