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- PDB-7bqo: The structure of HpiI in complex with its substrate analogue -

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Basic information

Entry
Database: PDB / ID: 7bqo
TitleThe structure of HpiI in complex with its substrate analogue
ComponentsHpiI
KeywordsBIOSYNTHETIC PROTEIN / pericyclase
Function / homology
Function and homology information


secondary metabolite biosynthetic process / O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-F56 / IMIDAZOLE / O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesHymenoscyphus scutula (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCai, Y.J. / Ohashi, M. / Zhou, J.H. / Tang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)91856202 China
Ministry of Science and Technology (MoST, China)2018YFA0901900 China
CitationJournal: Nature / Year: 2020
Title: An enzymatic Alder-ene reaction.
Authors: Ohashi, M. / Jamieson, C.S. / Cai, Y. / Tan, D. / Kanayama, D. / Tang, M.C. / Anthony, S.M. / Chari, J.V. / Barber, J.S. / Picazo, E. / Kakule, T.B. / Cao, S. / Garg, N.K. / Zhou, J. / Houk, K.N. / Tang, Y.
History
DepositionMar 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HpiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8135
Polymers52,1061
Non-polymers7074
Water8,179454
1
A: HpiI
hetero molecules

A: HpiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,62610
Polymers104,2122
Non-polymers1,4148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_857-x+3,y,-z+5/21
Buried area11550 Å2
ΔGint-58 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.113, 145.917, 90.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HpiI


Mass: 52106.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hymenoscyphus scutula (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1F8A906*PLUS

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Non-polymers , 5 types, 458 molecules

#2: Chemical ChemComp-F56 / 3-[(E,2S,4S)-2,4-dimethyloct-6-enoyl]-4-oxidanyl-1H-pyridin-2-one


Mass: 263.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#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
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 16% PEG8000, 40mM potassium phosphate monobasic, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.53→19.721 Å / Num. obs: 96254 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Net I/σ(I): 20.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.53-1.5612.31.0775772147090.860.3211.1252.699.9
8.38-19.72130.0479326100.9990.0120.04256.292.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.2.8data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BQJ

7bqj


Resolution: 1.53→19.721 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.86
RfactorNum. reflection% reflection
Rfree0.1824 4815 5 %
Rwork0.166 --
obs0.1668 96212 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.47 Å2 / Biso mean: 18.6347 Å2 / Biso min: 8.59 Å2
Refinement stepCycle: final / Resolution: 1.53→19.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 49 454 4078
Biso mean--31.94 25.15 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183708
X-RAY DIFFRACTIONf_angle_d1.5125021
X-RAY DIFFRACTIONf_chiral_restr0.33551
X-RAY DIFFRACTIONf_plane_restr0.011648
X-RAY DIFFRACTIONf_dihedral_angle_d11.1773082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.53-1.54740.30721690.29273003
1.5474-1.56560.26251370.24483052
1.5656-1.58470.23241400.22643008
1.5847-1.60470.24541680.20672993
1.6047-1.62580.24291600.21023037
1.6258-1.64810.23341460.20333013
1.6481-1.67160.20161560.18753063
1.6716-1.69650.2121860.17733001
1.6965-1.7230.19831450.16453026
1.723-1.75130.18321700.16433010
1.7513-1.78150.16331640.16083001
1.7815-1.81380.19821530.16213033
1.8138-1.84870.19791470.16313037
1.8487-1.88640.19241550.16573038
1.8864-1.92740.19311710.16723020
1.9274-1.97220.1791470.16913046
1.9722-2.02140.19951700.16853027
2.0214-2.0760.19731320.1633065
2.076-2.13710.16911740.16163052
2.1371-2.2060.17461470.15383064
2.206-2.28470.1791730.15723017
2.2847-2.3760.15311620.15113050
2.376-2.4840.18111560.16523042
2.484-2.61460.17491680.1683057
2.6146-2.7780.17541560.16623060
2.778-2.99190.20721620.17023093
2.9919-3.29170.16081760.16973062
3.2917-3.76510.1611730.15883080
3.7651-4.73280.16861910.14563103
4.7328-19.7210.18221610.15913244

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