[English] 日本語
Yorodumi
- PDB-2e1t: Crystal structure of Dendranthema morifolium DmAT complexed with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2e1t
TitleCrystal structure of Dendranthema morifolium DmAT complexed with malonyl-CoA
Componentsacyl transferase
KeywordsTRANSFERASE / BAHD superfamily / malonyl-CoA complex / acyl transferase / Dendranthema morifolium / DmAT
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONYL-COENZYME A / Anthocyanin malonyltransferase homolog
Similarity search - Component
Biological speciesChrysanthemum x morifolium (florist's daisy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUnno, H. / Ichimaida, F. / Kusunoki, M. / Nakayama, T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and Mutational Studies of Anthocyanin Malonyltransferases Establish the Features of BAHD Enzyme Catalysis
Authors: Unno, H. / Ichimaida, F. / Suzuki, H. / Takahashi, S. / Tanaka, Y. / Saito, A. / Nishino, T. / Kusunoki, M. / Nakayama, T.
History
DepositionOct 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: acyl transferase
B: acyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4284
Polymers101,7202
Non-polymers1,7072
Water8,341463
1
A: acyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7142
Polymers50,8601
Non-polymers8541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7142
Polymers50,8601
Non-polymers8541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.646, 122.922, 69.848
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEASPASPAA6 - 3646 - 364
21ILEILEASPASPBB6 - 3646 - 364
32ASNASNLEULEUAA370 - 450370 - 450
42ASNASNLEULEUBB370 - 450370 - 450
Detailsmonomer, for two molecules in the asymmetric

-
Components

#1: Protein acyl transferase


Mass: 50860.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chrysanthemum x morifolium (florist's daisy)
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: A4PHY4, Transferases
#2: Chemical ChemComp-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 8000, 10% glycerol, 0.12M ammonium sulfate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49363 / % possible obs: 95.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.8 / % possible all: 74.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E1V

2e1v


Resolution: 2.1→35.49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.12 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23363 2520 5.1 %RANDOM
Rwork0.19601 ---
obs0.19793 46812 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.001 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20.54 Å2
2---2.2 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 0 108 463 7503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227212
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9849812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89524.248306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.783151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3281534
X-RAY DIFFRACTIONr_chiral_restr0.1120.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025390
X-RAY DIFFRACTIONr_nbd_refined0.2140.23281
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2543
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.215
X-RAY DIFFRACTIONr_mcbond_it0.8041.54518
X-RAY DIFFRACTIONr_mcangle_it1.37227154
X-RAY DIFFRACTIONr_scbond_it1.85333056
X-RAY DIFFRACTIONr_scangle_it3.0914.52658
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1760tight positional0.050.05
1706loose positional0.365
1760tight thermal0.140.5
1706loose thermal0.8710
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 146 -
Rwork0.217 2552 -
obs--71.62 %

+
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