[English] 日本語
Yorodumi
- PDB-5dlk: The crystal structure of CT mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dlk
TitleThe crystal structure of CT mutant
ComponentsTqaA
KeywordsUNKNOWN FUNCTION / Biochemistry / mutant
Function / homology
Function and homology information


: / organic substance biosynthetic process / phosphopantetheine binding / ligase activity
Similarity search - Function
Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase ...Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Biological speciesPenicillium aethiopicum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, J.R. / Tang, Y. / Zhou, J.H.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural basis of nonribosomal peptide macrocyclization in fungi
Authors: Zhang, J. / Liu, N. / Cacho, R.A. / Gong, Z. / Liu, Z. / Qin, W. / Tang, C. / Tang, Y. / Zhou, J.
History
DepositionSep 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TqaA
B: TqaA
C: TqaA
D: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,42530
Polymers214,6824
Non-polymers1,74226
Water25,1311395
1
A: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1999
Polymers53,6711
Non-polymers5298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1999
Polymers53,6711
Non-polymers5298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0757
Polymers53,6711
Non-polymers4056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TqaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9515
Polymers53,6711
Non-polymers2804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.640, 221.678, 99.780
Angle α, β, γ (deg.)90.00, 127.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-663-

HOH

-
Components

#1: Protein
TqaA


Mass: 53670.582 Da / Num. of mol.: 4 / Fragment: UNP residues 3595-4074 / Mutation: residues 3992-4001 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium aethiopicum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F1CWE4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1395 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Sodium malnate, Bis-Tris propane, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 256485 / % possible obs: 99.9 % / Redundancy: 5.6 % / Net I/σ(I): 22.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DIJ

5dij


Resolution: 1.8→41.906 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 12863 5.02 %
Rwork0.1929 --
obs0.1944 256012 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→41.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14083 0 104 1395 15582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714606
X-RAY DIFFRACTIONf_angle_d1.09619917
X-RAY DIFFRACTIONf_dihedral_angle_d13.715254
X-RAY DIFFRACTIONf_chiral_restr0.0462259
X-RAY DIFFRACTIONf_plane_restr0.0062557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-1.82030.31364380.29077850X-RAY DIFFRACTION97
1.8203-1.84170.32844570.27898092X-RAY DIFFRACTION100
1.8417-1.86420.29274230.26578103X-RAY DIFFRACTION100
1.8642-1.88780.25544210.25178147X-RAY DIFFRACTION100
1.8878-1.91260.29074220.2568182X-RAY DIFFRACTION100
1.9126-1.93880.29254320.25178017X-RAY DIFFRACTION100
1.9388-1.96650.24274080.22898131X-RAY DIFFRACTION100
1.9665-1.99590.24154350.22428120X-RAY DIFFRACTION100
1.9959-2.02710.2414340.22818104X-RAY DIFFRACTION100
2.0271-2.06030.25234600.22258035X-RAY DIFFRACTION100
2.0603-2.09580.27234400.22588100X-RAY DIFFRACTION100
2.0958-2.13390.26464350.21488082X-RAY DIFFRACTION100
2.1339-2.1750.24784190.21238164X-RAY DIFFRACTION100
2.175-2.21940.25544210.21048109X-RAY DIFFRACTION100
2.2194-2.26760.2654230.22618093X-RAY DIFFRACTION100
2.2676-2.32040.23764630.20648118X-RAY DIFFRACTION100
2.3204-2.37840.2364140.2078100X-RAY DIFFRACTION100
2.3784-2.44270.24814560.20548039X-RAY DIFFRACTION100
2.4427-2.51450.25813920.20428140X-RAY DIFFRACTION100
2.5145-2.59570.2494580.21048162X-RAY DIFFRACTION100
2.5957-2.68850.23784150.20298091X-RAY DIFFRACTION100
2.6885-2.79610.25234410.2038120X-RAY DIFFRACTION100
2.7961-2.92330.22624420.19948134X-RAY DIFFRACTION100
2.9233-3.07740.25214300.21478124X-RAY DIFFRACTION100
3.0774-3.27010.21644200.20478114X-RAY DIFFRACTION100
3.2701-3.52250.21314520.18898131X-RAY DIFFRACTION100
3.5225-3.87670.18134310.17388106X-RAY DIFFRACTION100
3.8767-4.43720.17683780.15078161X-RAY DIFFRACTION100
4.4372-5.58830.17783920.14518198X-RAY DIFFRACTION100
5.5883-41.91690.16534110.15048082X-RAY DIFFRACTION98

+
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