[English] 日本語
Yorodumi
- PDB-5dua: First condensation domain of the calcium-dependent antibiotic syn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dua
TitleFirst condensation domain of the calcium-dependent antibiotic synthetase in complex with substrate analogue 3a
ComponentsCDA peptide synthetase I
Keywordsphosphopantetheine binding protein / Nonribosomal peptide synthetase / condensation domain / chemical probe / substrate analogue
Function / homology
Function and homology information


: / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity / cytosol
Similarity search - Function
Nonribosomal peptide synthetase, condensation domain / Non-ribosomal peptide synthase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Nonribosomal peptide synthetase, condensation domain / Non-ribosomal peptide synthase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-pentyl-L-alaninamide / CDA peptide synthetase I
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBloudoff, K. / Alonzo, D.A. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106615 Canada
CitationJournal: Cell Chem Biol / Year: 2016
Title: Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.
Authors: Bloudoff, K. / Alonzo, D.A. / Schmeing, T.M.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CDA peptide synthetase I
B: CDA peptide synthetase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3695
Polymers97,0172
Non-polymers3523
Water19,9431107
1
B: CDA peptide synthetase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7023
Polymers48,5091
Non-polymers1942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: CDA peptide synthetase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6672
Polymers48,5091
Non-polymers1581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.789, 83.479, 177.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CDA peptide synthetase I


Mass: 48508.500 Da / Num. of mol.: 2 / Fragment: UNP residues1-449 / Mutation: E17C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO3230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z4X6
#2: Chemical ChemComp-5FQ / N-pentyl-L-alaninamide


Type: L-peptide linking / Mass: 158.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1107 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25-27% PEG 3000, 0.2-0.25M Lithium sulfate, 0.1 M HEPES, PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→75.84 Å / Num. obs: 75270 / % possible obs: 97.6 % / Redundancy: 5.2 % / Net I/σ(I): 4.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.9→50.179 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1455 2.01 %
Rwork0.177 --
obs0.1779 71276 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→50.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 23 1107 7772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086826
X-RAY DIFFRACTIONf_angle_d1.0689304
X-RAY DIFFRACTIONf_dihedral_angle_d12.2752479
X-RAY DIFFRACTIONf_chiral_restr0.0391041
X-RAY DIFFRACTIONf_plane_restr0.0051241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93280.35981270.30846240X-RAY DIFFRACTION90
1.9328-1.96790.28271250.27656364X-RAY DIFFRACTION91
1.9679-2.00580.27491300.23036416X-RAY DIFFRACTION92
2.0058-2.04670.26691340.20886586X-RAY DIFFRACTION94
2.0467-2.09120.27321410.20726698X-RAY DIFFRACTION96
2.0912-2.13990.27811360.21036769X-RAY DIFFRACTION98
2.1399-2.19340.23711410.22246892X-RAY DIFFRACTION99
2.1934-2.25270.30341390.23166912X-RAY DIFFRACTION100
2.2527-2.3190.25831440.21217007X-RAY DIFFRACTION100
2.319-2.39380.23681420.18436932X-RAY DIFFRACTION100
2.3938-2.47940.25821440.18296944X-RAY DIFFRACTION100
2.4794-2.57860.25751360.17276924X-RAY DIFFRACTION100
2.5786-2.6960.23271410.17447003X-RAY DIFFRACTION100
2.696-2.83810.24941450.17286981X-RAY DIFFRACTION100
2.8381-3.01590.20551410.17746952X-RAY DIFFRACTION100
3.0159-3.24870.22121410.16916952X-RAY DIFFRACTION100
3.2487-3.57560.20971410.15836955X-RAY DIFFRACTION100
3.5756-4.09280.15831500.14436946X-RAY DIFFRACTION100
4.0928-5.15560.17241440.13376976X-RAY DIFFRACTION100
5.1556-50.19680.19031500.16326851X-RAY DIFFRACTION99

+
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://pdbjlvh1.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