[English] 日本語
Yorodumi
- PDB-2e1v: Crystal structure of Dendranthema morifolium DmAT, seleno-methion... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2e1v
TitleCrystal structure of Dendranthema morifolium DmAT, seleno-methionine derivative
Componentsacyl transferase
KeywordsTRANSFERASE / BAHD superfamily / acyl transferase / seleno-methionine derivative / Dendranthema morifolium / DmAT
Function / homology: / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / acyltransferase activity, transferring groups other than amino-acyl groups / 2-Layer Sandwich / Alpha Beta / Anthocyanin malonyltransferase homolog
Function and homology information
Biological speciesChrysanthemum x morifolium (florist's daisy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: acyl transferase
B: acyl transferase


Theoretical massNumber of molelcules
Total (without water)102,4712
Polymers102,4712
Non-polymers00
Water17,042946
1
A: acyl transferase


Theoretical massNumber of molelcules
Total (without water)51,2351
Polymers51,2351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acyl transferase


Theoretical massNumber of molelcules
Total (without water)51,2351
Polymers51,2351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.777, 122.908, 70.332
Angle α, β, γ (deg.)90.00, 94.38, 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

-
Components

#1: Protein acyl transferase


Mass: 51235.379 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 946 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 20% glycerol, 0.2M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97909, 0.97928, 0.95000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979091
20.979281
30.951
ReflectionResolution: 1.8→50 Å / Num. obs: 81316 / % possible obs: 98.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 24.275 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 31.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 5.3 / % possible all: 93

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30.46 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.924 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23376 4079 5 %RANDOM
Rwork0.19559 ---
obs0.19753 77222 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.726 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 0 0 946 7878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227100
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9679646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1525876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15424.248306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.499151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7041534
X-RAY DIFFRACTIONr_chiral_restr0.0790.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025336
X-RAY DIFFRACTIONr_nbd_refined0.2010.23568
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2795
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.234
X-RAY DIFFRACTIONr_mcbond_it0.711.54510
X-RAY DIFFRACTIONr_mcangle_it1.16627154
X-RAY DIFFRACTIONr_scbond_it1.6432919
X-RAY DIFFRACTIONr_scangle_it2.4994.52492
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 positional0.040.05
1706loose positional0.495
1760tight thermal0.190.5
1706loose thermal0.7610
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 263 -
Rwork0.242 5217 -
obs--90.95 %

+
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