[English] 日本語
Yorodumi
- PDB-1tuw: Structural and Functional Analysis of Tetracenomycin F2 Cyclase f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tuw
TitleStructural and Functional Analysis of Tetracenomycin F2 Cyclase from Streptomyces glaucescens: A Type-II Polyketide Cyclase
ComponentsTetracenomycin polyketide synthesis protein tcmI
KeywordsUNKNOWN FUNCTION / dimeric ??? ferredoxin-like fold tetracenomycin C biosynthesis
Function / homology
Function and homology information


tetracenomycin F2 cyclase / polyketide biosynthetic process / antibiotic biosynthetic process / lyase activity
Similarity search - Function
Dimeric alpha+beta barrel. / Polyketide synthesis cyclase / Polyketide synthesis cyclase superfamily / Polyketide synthesis cyclase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tetracenomycin F2 cyclase
Similarity search - Component
Biological speciesStreptomyces glaucescens (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.9 Å
AuthorsThompson, T.B. / Katayama, K. / Watanabe, K. / Hutchinson, C.R. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural and functional analysis of tetracenomycin F2 cyclase from Streptomyces glaucescens. A type II polyketide cyclase.
Authors: Thompson, T.B. / Katayama, K. / Watanabe, K. / Hutchinson, C.R. / Rayment, I.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tetracenomycin polyketide synthesis protein tcmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9742
Polymers12,8771
Non-polymers961
Water1,42379
1
A: Tetracenomycin polyketide synthesis protein tcmI
hetero molecules

A: Tetracenomycin polyketide synthesis protein tcmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9474
Polymers25,7552
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area4420 Å2
ΔGint-68 kcal/mol
Surface area10670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.7, 46.7, 188.3
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Tetracenomycin polyketide synthesis protein tcmI


Mass: 12877.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces glaucescens (bacteria) / Gene: TCMI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39890
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 278 K / Method: microbatch / pH: 7.5
Details: Crystals of tetracenomycin F2 cyclase were grown by microbatch from a solution composed of 2.2 M (NH4)2SO4, 3 mg/ml protein, 50 mM HEPES pH 7.5 at 4 C (11). Large crystals were obtained by ...Details: Crystals of tetracenomycin F2 cyclase were grown by microbatch from a solution composed of 2.2 M (NH4)2SO4, 3 mg/ml protein, 50 mM HEPES pH 7.5 at 4 C (11). Large crystals were obtained by macroseeding with small crystals (0.06 mm x 0.08 mm) washed in macroseeding 1.4 M (NH4)2SO4, 50 mM HEPES pH 7.5 to slightly dissolve the crystal surfaces. After 3 to 4 weeks the crystals attained a size of 0.3 x 0.3 x 0.6 mm. Crystals of the selenomethionine labeled protein were obtained in a similar manner., Micro batch, temperature 278K

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Mar 1, 2000 / Details: gobel
RadiationMonochromator: Gobel mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 11605 / Num. obs: 11355 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 23.1
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 5.4 / % possible all: 84

-
Processing

Software
NameClassification
Histardata collection
XDSdata reduction
SOLVEphasing
TNTrefinement
HISTARdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.245 480 random
Rwork0.199 --
all0.199 9599 -
obs0.199 9599 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 5 79 934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.61
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_dihedral_angle_d19.3

+
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