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- PDB-7yav: Crystal structure of Diels-Alderase MaDA1 -

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Basic information

Entry
Database: PDB / ID: 7yav
TitleCrystal structure of Diels-Alderase MaDA1
ComponentsMaDA1
KeywordsPLANT PROTEIN / natural product biosynthetic enzyme
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesMorus alba (white mulberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLei, X.G. / Chen, R.C. / Du, X.X. / Yang, J. / Fan, J.P. / Guo, N.X. / Ding, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22193073 China
National Natural Science Foundation of China (NSFC)91853202 China
CitationJournal: To Be Published
Title: Crystal structure of Diels-Alderase MaDA1
Authors: Lei, X.G. / Ding, Q. / Guo, N.X. / Yang, J. / Fan, J.P.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MaDA1
A: MaDA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5457
Polymers122,3102
Non-polymers2,2355
Water10,178565
1
B: MaDA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1623
Polymers61,1551
Non-polymers1,0072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MaDA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3834
Polymers61,1551
Non-polymers1,2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.783, 104.521, 141.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MaDA1


Mass: 61155.113 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.: 3 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 5.5) and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 71677 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.993 / CC star: 0.998 / Net I/σ(I): 4.7
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 3567 / CC1/2: 0.863 / CC star: 0.963

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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
Starting model: 7E2V

7e2v


Resolution: 2.1→20 Å / SU ML: 0.2069 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2262 1999 2.89 %
Rwork0.1951 67263 -
obs0.196 69262 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8011 0 148 565 8724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00768371
X-RAY DIFFRACTIONf_angle_d0.848811367
X-RAY DIFFRACTIONf_chiral_restr0.05661232
X-RAY DIFFRACTIONf_plane_restr0.00751435
X-RAY DIFFRACTIONf_dihedral_angle_d13.29863023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.24171170.18873915X-RAY DIFFRACTION79.51
2.16-2.220.22841270.18534307X-RAY DIFFRACTION87.85
2.22-2.280.23831340.20294492X-RAY DIFFRACTION91.37
2.28-2.350.26161380.19114642X-RAY DIFFRACTION94.32
2.35-2.440.25581450.194884X-RAY DIFFRACTION98.47
2.44-2.540.2441450.18284886X-RAY DIFFRACTION99.51
2.54-2.650.21631470.18854924X-RAY DIFFRACTION99.67
2.65-2.790.26021470.18394938X-RAY DIFFRACTION99.88
2.79-2.960.22661470.18614978X-RAY DIFFRACTION99.82
2.96-3.190.20361490.18614971X-RAY DIFFRACTION100
3.19-3.510.21051490.19045001X-RAY DIFFRACTION100
3.51-4.020.20741490.1875017X-RAY DIFFRACTION100
4.02-5.050.19781500.18815047X-RAY DIFFRACTION100
5.05-200.25651550.24075261X-RAY DIFFRACTION99.94

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