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- PDB-7dmo: Crystal structures of two pericyclases catalyzing [4+2] cycloadditions -

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Basic information

Entry
Database: PDB / ID: 7dmo
TitleCrystal structures of two pericyclases catalyzing [4+2] cycloadditions
ComponentsDiels-Alderase
KeywordsISOMERASE / [4+2]-pericyclase / BIOSYNTHETIC PROTEIN
Function / homology: / Diels-Alderase, C-terminal domain / Diels-Alderase N-terminal domain / Isomerases; Intramolecular lyases / isomerase activity / Diels-Alderase phm7
Function and homology information
Biological speciesPyrenochaetopsis sp. (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Z.D. / Chi, C.B. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFC0312502 China
CitationJournal: Acs Omega / Year: 2021
Title: Crystal Structures of Fsa2 and Phm7 Catalyzing [4 + 2] Cycloaddition Reactions with Reverse Stereoselectivities in Equisetin and Phomasetin Biosynthesis.
Authors: Chi, C. / Wang, Z. / Liu, T. / Zhang, Z. / Zhou, H. / Li, A. / Jin, H. / Jia, H. / Yin, F. / Yang, D. / Ma, M.
History
DepositionDec 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diels-Alderase
B: Diels-Alderase
C: Diels-Alderase
D: Diels-Alderase
E: Diels-Alderase
F: Diels-Alderase


Theoretical massNumber of molelcules
Total (without water)250,5126
Polymers250,5126
Non-polymers00
Water33,9221883
1
A: Diels-Alderase
E: Diels-Alderase

B: Diels-Alderase
F: Diels-Alderase

C: Diels-Alderase
D: Diels-Alderase


Theoretical massNumber of molelcules
Total (without water)250,5126
Polymers250,5126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area11190 Å2
ΔGint-65 kcal/mol
Surface area81090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.196, 150.533, 100.047
Angle α, β, γ (deg.)90.000, 96.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Diels-Alderase


Mass: 41752.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrenochaetopsis sp. (fungus) / Gene: phm7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2Z5XAU0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1883 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 7.0, 1.36 M Sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.540562 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 2→13.43 Å / Num. obs: 179300 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.33
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 3.43 / Num. unique obs: 17930 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DMN

7dmn


Resolution: 2→13.43 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 1853 1.1 %
Rwork0.1731 166047 -
obs0.1735 167900 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.33 Å2 / Biso mean: 24.8808 Å2 / Biso min: 9.91 Å2
Refinement stepCycle: final / Resolution: 2→13.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17039 0 0 1883 18922
Biso mean---30.82 -
Num. residues----2247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.2351320.19111193188
2.05-2.110.25381220.18681219689
2.11-2.180.241320.18311224690
2.18-2.260.24381410.18071243191
2.26-2.350.27241410.19151257192
2.35-2.460.22611440.18761258792
2.46-2.580.24741450.19491276594
2.58-2.750.19971430.18231292695
2.75-2.960.1981520.17821315096
2.96-3.250.20821480.17411327897
3.25-3.710.181540.1581340998
3.71-4.640.18321540.14591339498

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