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- PDB-7bql: The crystal structure of PdxI complex with the Alder-ene adduct -

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Basic information

Entry
Database: PDB / ID: 7bql
TitleThe crystal structure of PdxI complex with the Alder-ene adduct
ComponentsMethyltransf_2 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / pericyclase
Function / homology
Function and homology information


O-methyltransferase activity / secondary metabolite biosynthetic process / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-F5F / DI(HYDROXYETHYL)ETHER / O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesAspergillus bombycis (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 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 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransf_2 domain-containing protein
B: Methyltransf_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9206
Polymers103,2132
Non-polymers7074
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-61 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.075, 86.075, 291.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 60 or resid 62 through 171 or resid 173 through 459))
21(chain B and (resid 2 through 60 or resid 62...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEU(chain A and (resid 2 through 60 or resid 62 through 171 or resid 173 through 459))AA2 - 602 - 60
12ASNASNSERSER(chain A and (resid 2 through 60 or resid 62 through 171 or resid 173 through 459))AA62 - 17162 - 171
13LYSLYSGLUGLU(chain A and (resid 2 through 60 or resid 62 through 171 or resid 173 through 459))AA173 - 459173 - 459
21VALVALLEULEU(chain B and (resid 2 through 60 or resid 62...BB2 - 602 - 60
22ASNASNSERSER(chain B and (resid 2 through 60 or resid 62...BB62 - 17162 - 171
23LYSLYSASPASP(chain B and (resid 2 through 60 or resid 62...BB173 - 377173 - 377
24GLUGLUGLUGLU(chain B and (resid 2 through 60 or resid 62...BB389 - 459389 - 459

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Components

#1: Protein Methyltransf_2 domain-containing protein / PdxI


Mass: 51606.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus bombycis (mold) / Gene: ABOM_002889 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1F8A906
#2: Chemical ChemComp-F5F / 3-[(1R,2S,4R,6S)-2-ethenyl-4,6-dimethyl-cyclohexyl]-4-oxidanyl-1H-pyridin-2-one


Mass: 247.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 20000, 20% PEG MME 550, 0.1M MOPS/HEPES-Na pH 7.5, 0.02M of each alcohol (0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M (RS)-1,2-propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.396→50 Å / Num. obs: 43666 / % possible obs: 98.83 % / Redundancy: 4.419 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1189 / Rpim(I) all: 0.063 / Rrim(I) all: 0.135 / Net I/σ(I): 9.58
Reflection shellResolution: 2.396→2.482 Å / Redundancy: 4.582 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 6794 / CC1/2: 0.787 / Rpim(I) all: 0.3317 / Rrim(I) all: 0.68 / % possible all: 97.3

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Processing

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

7bqj


Resolution: 2.396→48.219 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 2182 5 %
Rwork0.199 41460 -
obs0.2006 43642 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.07 Å2 / Biso mean: 35.9831 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.396→48.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7145 0 50 237 7432
Biso mean--40.47 34.97 -
Num. residues----905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057393
X-RAY DIFFRACTIONf_angle_d0.69610038
X-RAY DIFFRACTIONf_chiral_restr0.0481090
X-RAY DIFFRACTIONf_plane_restr0.0051307
X-RAY DIFFRACTIONf_dihedral_angle_d21.1782716
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4257X-RAY DIFFRACTION5.56TORSIONAL
12B4257X-RAY DIFFRACTION5.56TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkRefine-ID% reflection obs (%)
2.396-2.48120.30090.2483X-RAY DIFFRACTION99
2.4812-2.58060.29590.2346X-RAY DIFFRACTION99
2.5806-2.6980.32210.2324X-RAY DIFFRACTION99
2.698-2.84020.25720.241X-RAY DIFFRACTION99
2.8402-3.01820.2730.2263X-RAY DIFFRACTION99
3.0182-3.25110.27740.2209X-RAY DIFFRACTION99
3.2511-3.57820.23790.2056X-RAY DIFFRACTION99
3.5782-4.09580.20720.1777X-RAY DIFFRACTION100
4.0958-5.15930.16960.1591X-RAY DIFFRACTION99
5.1593-48.2190.19550.1857X-RAY DIFFRACTION98

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