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- PDB-7x36: Crystal Structure of hetero-Diels-Alderase EupfF -

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Basic information

Entry
Database: PDB / ID: 7x36
TitleCrystal Structure of hetero-Diels-Alderase EupfF
ComponentsEupfF
KeywordsBIOSYNTHETIC PROTEIN / hetero-Diels-Alderase
Function / homologyBENZOIC ACID / alpha-D-mannopyranose / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsZhou, J. / Lu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91856202 China
CitationJournal: To Be Published
Title: Calcium-dependent glycosylated enzyme in the tandem hetero-Diels-Alder reaction
Authors: Zhou, J. / Lu, J.
History
DepositionFeb 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: 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

Downloads & links

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Assembly

Deposited unit
A: EupfF
B: EupfF
C: EupfF
D: EupfF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,50446
Polymers165,5304
Non-polymers8,97542
Water20,6451146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.944, 76.526, 147.781
Angle α, β, γ (deg.)90.000, 104.029, 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
EupfF


Mass: 41382.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium janthinellum (fungus) / Production host: Escherichia coli (E. coli)

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Sugars , 5 types, 18 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / 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
#11: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 1170 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O2
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1146 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.95 Å3/Da / Density % sol: 58.29 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate, PH=5.0, 20%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.92→46.9 Å / Num. obs: 146341 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.059 / Rrim(I) all: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2 / Num. unique obs: 7184 / CC1/2: 0.848 / Rpim(I) all: 0.515 / Rrim(I) all: 0.871 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X2N

7x2n


Resolution: 1.92→46.9 Å / SU ML: 0.2514 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2446 7176 4.95 %
Rwork0.2044 137774 -
obs0.2064 144950 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.09 Å2
Refinement stepCycle: LAST / Resolution: 1.92→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10682 0 586 1146 12414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008611582
X-RAY DIFFRACTIONf_angle_d0.934215850
X-RAY DIFFRACTIONf_chiral_restr0.06171836
X-RAY DIFFRACTIONf_plane_restr0.00691993
X-RAY DIFFRACTIONf_dihedral_angle_d10.50771732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.940.52192040.49994338X-RAY DIFFRACTION94.04
1.94-1.960.41972430.34174548X-RAY DIFFRACTION97.92
1.96-1.990.33972410.26464607X-RAY DIFFRACTION99.28
1.99-2.010.31662350.25044608X-RAY DIFFRACTION99.12
2.01-2.040.29912320.25294541X-RAY DIFFRACTION98.9
2.04-2.070.27862380.23694539X-RAY DIFFRACTION96.76
2.07-2.10.26592400.21684573X-RAY DIFFRACTION99.88
2.1-2.130.25372550.20764666X-RAY DIFFRACTION99.86
2.13-2.160.26122380.2034609X-RAY DIFFRACTION99.81
2.16-2.20.26852180.21974630X-RAY DIFFRACTION99.69
2.2-2.240.41112180.33984189X-RAY DIFFRACTION90.29
2.24-2.280.47332160.40384506X-RAY DIFFRACTION95.94
2.28-2.320.33832110.27194352X-RAY DIFFRACTION93.95
2.32-2.370.26772320.19994626X-RAY DIFFRACTION99.77
2.37-2.420.26452180.19654660X-RAY DIFFRACTION99.47
2.42-2.480.26912200.20024632X-RAY DIFFRACTION99.04
2.48-2.540.27282440.20374590X-RAY DIFFRACTION98.55
2.54-2.610.24952820.1954597X-RAY DIFFRACTION99.92
2.61-2.680.24482740.19164604X-RAY DIFFRACTION99.92
2.68-2.770.25752630.19194654X-RAY DIFFRACTION99.96
2.77-2.870.24612420.18934646X-RAY DIFFRACTION99.92
2.87-2.980.23532380.19474640X-RAY DIFFRACTION99.88
2.98-3.120.22972240.18984682X-RAY DIFFRACTION99.74
3.12-3.280.21692520.18444629X-RAY DIFFRACTION98.81
3.28-3.490.21932610.19194632X-RAY DIFFRACTION99.9
3.49-3.760.22962440.19134610X-RAY DIFFRACTION99.22
3.76-4.140.18712330.16564708X-RAY DIFFRACTION99.6
4.14-4.730.17572490.14624676X-RAY DIFFRACTION99.29
4.73-5.960.17872550.15764705X-RAY DIFFRACTION99.56
5.96-46.90.22352560.19864777X-RAY DIFFRACTION99.04

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