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- PDB-8zls: Apo structure of BBE-like oxidative cyclase MaDS1 -

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Basic information

Entry
Database: PDB / ID: 8zls
TitleApo structure of BBE-like oxidative cyclase MaDS1
ComponentsMaDS1
KeywordsPLANT PROTEIN / BBE-like enzyme / Oxidative cyclase / FLAVOPROTEIN
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesMorus alba (white mulberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsGuo, N. / Fan, J. / Yang, 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. / Gu, J. / Zhou, Q. / Liu, F. / Dong, H. / Ding, Q. / Wang, Q. / Wu, D. / Yang, J. / Fan, J. / Gao, L. / Houk, K.N. / Lei, X.
History
DepositionMay 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)119,4204
Polymers117,8492
Non-polymers1,5712
Water6,197344
1
A: MaDS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7102
Polymers58,9241
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MaDS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7102
Polymers58,9241
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.244, 125.002, 85.229
Angle α, β, γ (deg.)90.000, 95.848, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris (pH 6.5), and 25% PEG mme 2000, and 0.1 M glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→26.48 Å / Num. obs: 54398 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.83 Å2 / CC1/2: 0.983 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.25 Å / Num. unique obs: 2670 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
CootCoot 0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→26.48 Å / SU ML: 0.2499 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2231 1994 3.67 %
Rwork0.1733 52280 -
obs0.1751 54274 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.62 Å2
Refinement stepCycle: LAST / Resolution: 2.21→26.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7975 0 106 344 8425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818286
X-RAY DIFFRACTIONf_angle_d0.906411226
X-RAY DIFFRACTIONf_chiral_restr0.05251201
X-RAY DIFFRACTIONf_plane_restr0.00791423
X-RAY DIFFRACTIONf_dihedral_angle_d7.00341095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.34231160.28733115X-RAY DIFFRACTION81.98
2.27-2.330.29821440.21783773X-RAY DIFFRACTION99.59
2.33-2.40.28371450.1873785X-RAY DIFFRACTION99.65
2.4-2.480.22961420.1853741X-RAY DIFFRACTION99.56
2.48-2.560.25281450.18223795X-RAY DIFFRACTION99.55
2.56-2.670.25031450.18663789X-RAY DIFFRACTION99.52
2.67-2.790.28471430.18163738X-RAY DIFFRACTION99.41
2.79-2.930.24371440.18033782X-RAY DIFFRACTION99.67
2.93-3.120.22961440.17913770X-RAY DIFFRACTION99.47
3.12-3.360.22821440.17483779X-RAY DIFFRACTION99.57
3.36-3.70.20641440.15953760X-RAY DIFFRACTION98.71
3.7-4.230.20031450.15143785X-RAY DIFFRACTION99.57
4.23-5.320.15211470.1373830X-RAY DIFFRACTION99.95
5.32-26.480.21061460.17923838X-RAY DIFFRACTION99.53

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