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- PDB-7e2v: Crystal structure of MaDA-3 -

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Basic information

Entry
Database: PDB / ID: 7e2v
TitleCrystal structure of MaDA-3
ComponentsMaDA-3
KeywordsPLANT PROTEIN / enzyme Diels-Alderase cycloaddition stereoselectivity
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesMorus alba (white mulberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsGao, L. / Du, X. / Fan, J. / Lei, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21625201 China
CitationJournal: Nat Catal / Year: 2021
Title: Enzymatic control of endo- and exo-stereoselective Diels-Alder reactions with broad substrate scope.
Authors: Gao, L. / Zou, Y. / Liu, X. / Yang, J. / Du, X. / Wang, J. / Yu, X. / Fan, J. / Jiang, M. / Li, Y. / Houk, K.N. / Lei, X.
History
DepositionFeb 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MaDA-3
B: MaDA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7886
Polymers124,7742
Non-polymers2,0144
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: crystal packing
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.028, 79.167, 95.011
Angle α, β, γ (deg.)90.000, 98.232, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 32 through 39 or (resid 40...
d_2ens_1(chain "B" and (resid 32 through 51 or (resid 52...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERILEA3 - 12
d_12ens_1GLUTHRA14 - 264
d_13ens_1ILELEUA272 - 321
d_14ens_1ASPASNA324 - 332
d_15ens_1ARGGLUA336 - 408
d_16ens_1ALAPROA414 - 453
d_17ens_1TYRPROA456 - 499
d_21ens_1SERPROE1 - 477

NCS oper: (Code: givenMatrix: (0.445438994483, -0.838450358181, -0.313982641336), (-0.859304009601, -0.498829168544, 0.112987077548), (-0.251357755555, 0.219477692432, -0.942681717892)Vector: 24. ...NCS oper: (Code: given
Matrix: (0.445438994483, -0.838450358181, -0.313982641336), (-0.859304009601, -0.498829168544, 0.112987077548), (-0.251357755555, 0.219477692432, -0.942681717892)
Vector: 24.7458188039, 52.9090325603, -33.6275185377)

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Components

#1: Protein MaDA-3


Mass: 62387.156 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 / Comment: FAD*YM
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: 50.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 10% 2-propanol, 0.1 M Bicine, pH 8.5, 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.94→43.59 Å / Num. obs: 25940 / % possible obs: 99.27 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.88 Å2 / Rpim(I) all: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 2.95→3 Å / Num. unique obs: 1246 / CC1/2: 0.841

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JQH

6jqh


Resolution: 2.94→43.59 Å / SU ML: 0.4997 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.0523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3082 1299 5.01 %
Rwork0.2668 24641 -
obs0.2689 25940 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.2 Å2
Refinement stepCycle: LAST / Resolution: 2.94→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7751 0 134 0 7885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00438077
X-RAY DIFFRACTIONf_angle_d0.926410968
X-RAY DIFFRACTIONf_chiral_restr0.05741220
X-RAY DIFFRACTIONf_plane_restr0.00591362
X-RAY DIFFRACTIONf_dihedral_angle_d211085
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.15607736955 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.060.36641390.29952633X-RAY DIFFRACTION97.3
3.06-3.20.34911430.30152729X-RAY DIFFRACTION99.97
3.2-3.370.33711450.29872746X-RAY DIFFRACTION99.83
3.37-3.580.38551440.3142723X-RAY DIFFRACTION99.24
3.58-3.850.3691440.30062732X-RAY DIFFRACTION99.21
3.85-4.240.31451430.27862720X-RAY DIFFRACTION99.24
4.24-4.850.26951450.22232774X-RAY DIFFRACTION99.97
4.85-6.110.27091470.24012760X-RAY DIFFRACTION99.38
6.11-43.590.25281490.24022824X-RAY DIFFRACTION99.33

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