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- PDB-7e5v: Crystal structure of Phm7 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7e5v
TitleCrystal structure of Phm7 in complex with inhibitor
ComponentsDiels-Alderase
KeywordsBIOSYNTHETIC PROTEIN / Cyclase / diels-alderase / diels alder / [4+2] cycloaddition
Function / homologyDiels-Alderase, C-terminal domain / Isomerases; Intramolecular lyases / isomerase activity / Chem-HZC / Diels-Alderase phm7
Function and homology information
Biological speciesPyrenochaetopsis sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsFujiyama, K. / Kato, N. / Kinugasa, K. / Hino, T. / Takahashi, S. / Nagano, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04665 Japan
Japan Society for the Promotion of Science (JSPS)19H05780 Japan
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*.
Authors: Fujiyama, K. / Kato, N. / Re, S. / Kinugasa, K. / Watanabe, K. / Takita, R. / Nogawa, T. / Hino, T. / Osada, H. / Sugita, Y. / Takahashi, S. / Nagano, S.
History
DepositionFeb 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,21529
Polymers125,2563
Non-polymers2,95926
Water14,268792
1
A: Diels-Alderase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2946
Polymers41,7521
Non-polymers5425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diels-Alderase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,91711
Polymers41,7521
Non-polymers1,16410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Diels-Alderase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,00512
Polymers41,7521
Non-polymers1,25311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.052, 149.881, 99.270
Angle α, β, γ (deg.)90.000, 97.119, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Diels-Alderase


Mass: 41752.055 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrenochaetopsis sp. (fungus) / Gene: phm7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z5XAU0
#2: Chemical
ChemComp-HZC / [(1S,2S,5R)-5-methyl-2-propan-2-yl-cyclohexyl]methanamine


Mass: 169.307 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C11H23N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.54-1.62M Ammonium sulfate, 0.1M Tris HCl, 14-19% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→45.216 Å / Num. obs: 169791 / % possible obs: 99.82 % / Redundancy: 3.5 % / CC1/2: 0.996 / Net I/σ(I): 12.59
Reflection shellResolution: 1.61→1.668 Å / Num. unique obs: 16956 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
pointless1.11.6data scaling
Aimless0.5.32data scaling
MLPHARE2.7.17phasing
Cootmodel building
REFMAC5.8.0258refinement
PHENIX1.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phm7

Resolution: 1.61→45.216 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.671 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2106 8514 5.014 %
Rwork0.1828 161276 -
all0.184 --
obs-169790 99.827 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.514 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å20 Å2-0.002 Å2
2--0.001 Å20 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.61→45.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8470 0 192 792 9454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138885
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177887
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.6512078
X-RAY DIFFRACTIONr_angle_other_deg1.4961.618344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.90151109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29622.899414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.564151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3381536
X-RAY DIFFRACTIONr_chiral_restr0.0870.21117
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021895
X-RAY DIFFRACTIONr_nbd_refined0.1990.21450
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.27541
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24165
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.24256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2606
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other00.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.227
X-RAY DIFFRACTIONr_nbd_other0.2060.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.225
X-RAY DIFFRACTIONr_mcbond_it2.5412.4884457
X-RAY DIFFRACTIONr_mcbond_other2.5412.4884456
X-RAY DIFFRACTIONr_mcangle_it3.8273.7245559
X-RAY DIFFRACTIONr_mcangle_other3.8273.7235560
X-RAY DIFFRACTIONr_scbond_it3.4472.8444427
X-RAY DIFFRACTIONr_scbond_other3.4452.8434420
X-RAY DIFFRACTIONr_scangle_it5.1124.1136519
X-RAY DIFFRACTIONr_scangle_other5.1074.1116508
X-RAY DIFFRACTIONr_lrange_it6.96230.2869588
X-RAY DIFFRACTIONr_lrange_other6.88429.829398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.6520.2645850.2511997X-RAY DIFFRACTION99.7463
1.652-1.6970.2785810.23411600X-RAY DIFFRACTION99.8688
1.697-1.7460.2555450.21611352X-RAY DIFFRACTION99.9664
1.746-1.80.2556330.20610932X-RAY DIFFRACTION99.9395
1.8-1.8590.2255380.19510658X-RAY DIFFRACTION99.9554
1.859-1.9240.2215220.18910297X-RAY DIFFRACTION99.9446
1.924-1.9970.2295260.1879967X-RAY DIFFRACTION99.9428
1.997-2.0780.2145230.1879493X-RAY DIFFRACTION99.9102
2.078-2.1710.214300.1819231X-RAY DIFFRACTION99.9897
2.171-2.2770.224440.1818801X-RAY DIFFRACTION99.9243
2.277-2.40.2244710.1778294X-RAY DIFFRACTION99.9658
2.4-2.5450.2214640.1837852X-RAY DIFFRACTION99.8799
2.545-2.7210.2063880.1747395X-RAY DIFFRACTION99.7309
2.721-2.9390.2153730.1816894X-RAY DIFFRACTION99.6982
2.939-3.2190.1963260.1796322X-RAY DIFFRACTION99.6403
3.219-3.5980.2073230.1755719X-RAY DIFFRACTION99.3913
3.598-4.1540.1893010.1675067X-RAY DIFFRACTION99.7213
4.154-5.0850.172530.1594251X-RAY DIFFRACTION99.5139
5.085-7.1820.2211760.2013324X-RAY DIFFRACTION99.4318
7.182-45.2160.2131120.1921830X-RAY DIFFRACTION98.5787

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