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- PDB-7w26: monolignol ferulate transferase -

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Basic information

Entry
Database: PDB / ID: 7w26
Titlemonolignol ferulate transferase
ComponentsFerulate monolignol transferase
KeywordsTRANSFERASE / enzyme / plant protein
Function / homology: / Transferase family / acyltransferase activity, transferring groups other than amino-acyl groups / Chloramphenicol acetyltransferase-like domain superfamily / Ferulate monolignol transferase
Function and homology information
Biological speciesAngelica sinensis (Chinese angelica)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsXi, L. / Shuliu, D. / Yue, F. / Yi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000901 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of the plant feruloyl-coenzyme A monolignol transferase provides insights into the formation of monolignol ferulate conjugates.
Authors: Liu, X. / Dai, S. / Zhou, Y. / Liu, J. / Li, D. / Zhang, J. / Zhu, Y. / Zhao, Q. / Feng, Y. / Zhang, Y.
History
DepositionNov 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferulate monolignol transferase
B: Ferulate monolignol transferase


Theoretical massNumber of molelcules
Total (without water)101,6242
Polymers101,6242
Non-polymers00
Water1,71195
1
A: Ferulate monolignol transferase


Theoretical massNumber of molelcules
Total (without water)50,8121
Polymers50,8121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferulate monolignol transferase


Theoretical massNumber of molelcules
Total (without water)50,8121
Polymers50,8121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.420, 136.420, 102.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 192 or resid 194 through 442))
21(chain B and (resid 4 through 192 or resid 194 through 442))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPHEPHE(chain A and (resid 4 through 192 or resid 194 through 442))AA4 - 1924 - 192
12LEULEULEULEU(chain A and (resid 4 through 192 or resid 194 through 442))AA194 - 442194 - 442
21METMETPHEPHE(chain B and (resid 4 through 192 or resid 194 through 442))BB4 - 1924 - 192
22LEULEULEULEU(chain B and (resid 4 through 192 or resid 194 through 442))BB194 - 442194 - 442

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Components

#1: Protein Ferulate monolignol transferase


Mass: 50811.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Angelica sinensis (Chinese angelica) / Production host: Escherichia coli (E. coli) / References: UniProt: W8NXL9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: potassium bromide, Tris, PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.43→96.46 Å / Num. obs: 37114 / % possible obs: 99.73 % / Redundancy: 6.78 % / CC1/2: 0.998 / Net I/σ(I): 13.25
Reflection shellResolution: 2.43→2.58 Å / Num. unique obs: 5867 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bgh

2bgh


Resolution: 2.43→96.46 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1847 4.99 %
Rwork0.2159 35181 -
obs0.2184 37028 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.63 Å2 / Biso mean: 61.3239 Å2 / Biso min: 24.58 Å2
Refinement stepCycle: final / Resolution: 2.43→96.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6971 0 0 95 7066
Biso mean---51.15 -
Num. residues----880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2642X-RAY DIFFRACTION9.255TORSIONAL
12B2642X-RAY DIFFRACTION9.255TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.50.41861160.3232631274798
2.5-2.570.35091440.29626742818100
2.57-2.650.31641270.281626622789100
2.65-2.750.34841520.26872662281499
2.75-2.860.32941360.264626772813100
2.86-2.990.3641450.277926652810100
2.99-3.140.3391250.260127122837100
3.14-3.340.27231560.238426892845100
3.34-3.60.28921410.213226792820100
3.6-3.960.24211770.194126822859100
3.96-4.530.20561480.170127382886100
4.54-5.710.22841370.174627852922100
5.71-96.460.23971430.206929253068100
Refinement TLS params.Method: refined / Origin x: 2.6811 Å / Origin y: 34.3728 Å / Origin z: -16.1161 Å
111213212223313233
T0.2898 Å20.0151 Å2-0.0198 Å2-0.2995 Å2-0.0053 Å2--0.3307 Å2
L0.164 °2-0.0405 °2-0.013 °2-0.1593 °20.0635 °2--0.5153 °2
S-0.0422 Å °0.0014 Å °0.0743 Å °0.003 Å °-0.0091 Å °0.0325 Å °-0.042 Å °-0.0245 Å °0.054 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 442
2X-RAY DIFFRACTION1allB3 - 442
3X-RAY DIFFRACTION1allS1 - 95

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