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- PDB-8zlt: Co-crystal structure of MaDS1 with diene -

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Basic information

Entry
Database: PDB / ID: 8zlt
TitleCo-crystal structure of MaDS1 with diene
ComponentsMaDS1
KeywordsPLANT PROTEIN / BBE-like enzyme / Oxidase / FLAVOPROTEIN
Function / homology: / FLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesMorus alba (white mulberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsGuo, N. / Yang, J. / Fan, J. / Lei, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22193073 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Aspartic acid residues in BBE-like enzymes from Morus alba promote a function shift from oxidative cyclization to dehydrogenation
Authors: Guo, N. / Fan, J. / Yang, J. / Lei, X.
History
DepositionMay 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MaDS1
B: MaDS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0246
Polymers117,8492
Non-polymers2,1764
Water10,124562
1
A: MaDS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0123
Polymers58,9241
Non-polymers1,0882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MaDS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0123
Polymers58,9241
Non-polymers1,0882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.392, 122.632, 84.050
Angle α, β, γ (deg.)90.000, 95.859, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein MaDS1


Mass: 58924.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morus alba (white mulberry) / Production host: Trichoplusia ni (cabbage looper)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-A1D8F / methyl 4-[(1~{E})-7-methyl-3-methylidene-octa-1,6-dienyl]-3,5-bis(oxidanyl)benzoate / 2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1,3,4-OXADIAZOLE


Mass: 302.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride 0.1 M BIS-TRIS pH 6.5 25% PEG 3350 additive: 0.1M Glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.03→49.4 Å / Num. obs: 67080 / % possible obs: 98.7 % / Redundancy: 6.58 % / Biso Wilson estimate: 25.15 Å2 / CC1/2: 0.997 / Net I/σ(I): 17.54
Reflection shellResolution: 2.03→2.08 Å / Rmerge(I) obs: 0.5242 / Mean I/σ(I) obs: 4.21 / Num. unique obs: 4989 / CC1/2: 0.8474 / Rpim(I) all: 0.2172 / Rrim(I) all: 0.5684

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CootCoot 0.8.9.2model building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→46.41 Å / SU ML: 0.2108 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 20.9863
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 2000 2.98 %
Rwork0.1667 65002 -
obs0.1683 67002 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.22 Å2
Refinement stepCycle: LAST / Resolution: 2.03→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7989 0 150 562 8701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00738344
X-RAY DIFFRACTIONf_angle_d0.902511307
X-RAY DIFFRACTIONf_chiral_restr0.05711206
X-RAY DIFFRACTIONf_plane_restr0.00751436
X-RAY DIFFRACTIONf_dihedral_angle_d7.54881121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.30511420.21174613X-RAY DIFFRACTION97.7
2.08-2.140.23451410.19164617X-RAY DIFFRACTION99.21
2.14-2.20.2391450.18264671X-RAY DIFFRACTION98.99
2.2-2.270.26531420.18344614X-RAY DIFFRACTION97.56
2.27-2.350.21281400.17314602X-RAY DIFFRACTION98.59
2.35-2.450.21241440.17014663X-RAY DIFFRACTION99.26
2.45-2.560.2331440.17034677X-RAY DIFFRACTION99.12
2.56-2.690.2381430.16784631X-RAY DIFFRACTION98.82
2.69-2.860.24581400.17144574X-RAY DIFFRACTION97.38
2.86-3.080.2211450.17284705X-RAY DIFFRACTION99.28
3.08-3.390.21921430.16544637X-RAY DIFFRACTION99.13
3.39-3.880.22111420.15384638X-RAY DIFFRACTION97.91
3.88-4.890.18261440.14334709X-RAY DIFFRACTION99.12
4.89-46.410.21450.17144651X-RAY DIFFRACTION97.16

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