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- PDB-7x2n: Crystal structure of Diels-Alderase PycR1 -

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Basic information

Entry
Database: PDB / ID: 7x2n
TitleCrystal structure of Diels-Alderase PycR1
ComponentsPycR1
KeywordsBIOSYNTHETIC PROTEIN / Diels-Alderase
Function / homologyalpha-D-mannopyranose
Function and homology information
Biological speciesLeptobacillium sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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: Crystal structure of hetero-Diels-Alderase PycR1
Authors: Zhou, J. / Lu, J.
History
DepositionFeb 25, 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
Revision 1.2Nov 13, 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: PycR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7619
Polymers42,9541
Non-polymers2,8078
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint27 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.321, 78.321, 164.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-909-

HOH

21A-1114-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PycR1


Mass: 42954.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptobacillium sp. (fungus) / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1072.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 , 4 types, 481 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-Sodium citrate, 20% (w/v)PEG4000, 5% (w/v)Isopropanol

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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 PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.72→45.89 Å / Num. obs: 55134 / % possible obs: 100 % / Redundancy: 25.7 % / Biso Wilson estimate: 28.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.023 / Net I/σ(I): 23.8
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 1.778 / Num. unique obs: 2891 / CC1/2: 0.806 / Rpim(I) all: 0.503 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p4o

2p4o


Resolution: 1.72→44.83 Å / SU ML: 0.179 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1863 2738 4.97 %
Rwork0.1605 52299 -
obs0.1618 55037 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.45 Å2
Refinement stepCycle: LAST / Resolution: 1.72→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 185 476 3355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01882974
X-RAY DIFFRACTIONf_angle_d1.47134067
X-RAY DIFFRACTIONf_chiral_restr0.1069483
X-RAY DIFFRACTIONf_plane_restr0.0103503
X-RAY DIFFRACTIONf_dihedral_angle_d14.1144498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.750.30071300.27312579X-RAY DIFFRACTION100
1.75-1.780.26731360.24252580X-RAY DIFFRACTION100
1.78-1.820.26081500.21432549X-RAY DIFFRACTION99.93
1.82-1.850.22681440.19462544X-RAY DIFFRACTION100
1.85-1.890.24021330.18682577X-RAY DIFFRACTION100
1.89-1.940.22081330.19542571X-RAY DIFFRACTION99.93
1.94-1.990.24871460.18762563X-RAY DIFFRACTION99.96
1.99-2.040.18381290.17362585X-RAY DIFFRACTION100
2.04-2.10.22411370.17332582X-RAY DIFFRACTION100
2.1-2.170.20541340.17212610X-RAY DIFFRACTION100
2.17-2.240.19331140.16582625X-RAY DIFFRACTION99.96
2.24-2.330.22281230.16122597X-RAY DIFFRACTION100
2.33-2.440.1851320.16912602X-RAY DIFFRACTION100
2.44-2.570.18961510.16642602X-RAY DIFFRACTION100
2.57-2.730.22191350.16362604X-RAY DIFFRACTION100
2.73-2.940.1791480.16432625X-RAY DIFFRACTION100
2.94-3.240.20011320.1592667X-RAY DIFFRACTION100
3.24-3.70.15971640.15352646X-RAY DIFFRACTION100
3.71-4.670.15641190.12752721X-RAY DIFFRACTION100
4.67-44.830.15641480.15262870X-RAY DIFFRACTION99.97

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