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- PDB-2e1u: Crystal structure of Dendranthema morifolium DmAT -

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Basic information

Entry
Database: PDB / ID: 2e1u
TitleCrystal structure of Dendranthema morifolium DmAT
Componentsacyl transferase
KeywordsTRANSFERASE / BAHD superfamily / acyl transferase / Dendranthema morifolium / DmAT
Function / homology: / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Anthocyanin malonyltransferase homolog
Function and homology information
Biological speciesChrysanthemum x morifolium (florist's daisy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / 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
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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: acyl transferase
B: acyl transferase


Theoretical massNumber of molelcules
Total (without water)101,7202
Polymers101,7202
Non-polymers00
Water12,556697
1
A: acyl transferase


Theoretical massNumber of molelcules
Total (without water)50,8601
Polymers50,8601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: acyl transferase


Theoretical massNumber of molelcules
Total (without water)50,8601
Polymers50,8601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.650, 122.982, 70.268
Angle α, β, γ (deg.)90.00, 94.21, 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

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 8000, 10% glycerol, 0.1M ammonium sulfate, 0.1M sodium cacodylate, 10% KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 2.2→50 Å / Num. obs: 40795 / % possible obs: 90.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 32.762 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.6 / % possible all: 59.2

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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: 2.2→33.88 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.37 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24829 2023 5 %RANDOM
Rwork0.19351 ---
obs0.1963 38744 89.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.12 Å2
2---0.13 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 0 0 697 7629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227100
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9679646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.424.248306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.032151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4881534
X-RAY DIFFRACTIONr_chiral_restr0.1120.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025336
X-RAY DIFFRACTIONr_nbd_refined0.2170.23443
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24867
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2683
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.228
X-RAY DIFFRACTIONr_mcbond_it0.7891.54512
X-RAY DIFFRACTIONr_mcangle_it1.37127154
X-RAY DIFFRACTIONr_scbond_it1.73832920
X-RAY DIFFRACTIONr_scangle_it2.7464.52492
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 positional0.050.05
1706loose positional0.55
1760tight thermal0.750.5
1706loose thermal1.2510
LS refinement shellResolution: 2.2→2.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 90 -
Rwork0.215 1579 -
obs--50.79 %

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