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- PDB-7bqj: The structure of PdxI -

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Basic information

Entry
Database: PDB / ID: 7bqj
TitleThe structure of PdxI
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
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / 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 ...Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / 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
Uncharacterized protein
Similarity search - Component
Biological speciesAspergillus bombycis (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 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 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)104,25115
Polymers103,2132
Non-polymers1,03813
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13890 Å2
ΔGint-77 kcal/mol
Surface area34750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.163, 87.163, 294.404
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 77 or resid 79...
21(chain B and (resid 2 through 77 or resid 79...

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
11VALVALASNASN(chain A and (resid 2 through 77 or resid 79...AA2 - 772 - 77
12LYSLYSPROPRO(chain A and (resid 2 through 77 or resid 79...AA79 - 9879 - 98
13ASPASPASPASP(chain A and (resid 2 through 77 or resid 79...AA100 - 377100 - 377
14ALAALAGLUGLU(chain A and (resid 2 through 77 or resid 79...AA384 - 459384 - 459
21VALVALASNASN(chain B and (resid 2 through 77 or resid 79...BB2 - 772 - 77
22LYSLYSPROPRO(chain B and (resid 2 through 77 or resid 79...BB79 - 9879 - 98
23ASPASPASPASP(chain B and (resid 2 through 77 or resid 79...BB100 - 377100 - 377
24ALAALAGLUGLU(chain B and (resid 2 through 77 or resid 79...BB384 - 459384 - 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 8000, 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: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 80965 / % possible obs: 100 % / Redundancy: 17.7 % / Biso Wilson estimate: 25.91 Å2 / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.074 / Rrim(I) all: 0.312 / Χ2: 0.983 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.0113.92.57439650.6030.7122.6730.926100
2.01-2.0514.42.23139950.6650.6062.3130.94100
2.05-2.0915.71.98339690.7490.5172.0510.945100
2.09-2.1317.51.77540040.8010.4381.8290.943100
2.13-2.1818.31.48239640.8490.3571.5260.959100
2.18-2.2318.71.33339710.8880.3181.3710.98100
2.23-2.2918.71.04240080.9270.2481.0720.974100
2.29-2.3518.50.85939690.9490.2050.8830.995100
2.35-2.4218.20.72640000.9540.1750.7471.018100
2.42-2.4917.20.59740170.9660.1480.6151.028100
2.49-2.5818.10.51540380.9780.1240.531.035100
2.58-2.6919.20.41640010.9850.0970.4281.038100
2.69-2.8118.90.34440320.9880.0810.3541.057100
2.81-2.9618.80.27940330.9890.0660.2871.034100
2.96-3.1418.10.21640600.9910.0520.2221.063100
3.14-3.3917.50.1640660.9940.0390.1651.064100
3.39-3.7319.20.12340870.9960.0290.1261.026100
3.73-4.2618.50.09741380.9970.0230.10.959100
4.26-5.3717.10.08441890.9970.0210.0860.896100
5.37-5016.90.07344590.9980.0180.0750.74999.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIX1.12_2829phasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→41.788 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.23
RfactorNum. reflection% reflection
Rfree0.2089 4025 5.02 %
Rwork0.1828 --
obs0.1841 80256 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.54 Å2 / Biso mean: 27.0662 Å2 / Biso min: 13.62 Å2
Refinement stepCycle: final / Resolution: 1.98→41.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7177 0 67 467 7711
Biso mean--38.71 28.95 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147433
X-RAY DIFFRACTIONf_angle_d1.08310070
X-RAY DIFFRACTIONf_chiral_restr0.0941088
X-RAY DIFFRACTIONf_plane_restr0.0071309
X-RAY DIFFRACTIONf_dihedral_angle_d4.7886161
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4356X-RAY DIFFRACTION5.75TORSIONAL
12B4356X-RAY DIFFRACTION5.75TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.98-1.99670.28151100.2505247094
1.9967-2.0210.28951400.2252253297
2.021-2.04660.26081320.2187251797
2.0466-2.07350.23321330.2171256397
2.0735-2.10190.26851270.2176249897
2.1019-2.13190.24031500.2092256098
2.1319-2.16380.2531330.2017257198
2.1638-2.19760.23081390.202255799
2.1976-2.23360.24891570.20282619100
2.2336-2.27210.20981210.20162575100
2.2721-2.31340.23341380.19162636100
2.3134-2.35790.23931250.19652653100
2.3579-2.4060.24231340.19542606100
2.406-2.45840.22721470.19572617100
2.4584-2.51550.20311390.1922614100
2.5155-2.57840.20671370.19622657100
2.5784-2.64810.20481350.19582616100
2.6481-2.72610.23341380.19522650100
2.7261-2.8140.23291570.19572631100
2.814-2.91460.22551330.19472635100
2.9146-3.03120.2061410.19342644100
3.0312-3.16920.23691340.19372669100
3.1692-3.33620.20711280.18322687100
3.3362-3.54510.20091460.1822658100
3.5451-3.81860.18771630.17492668100
3.8186-4.20260.16731470.15792703100
4.2026-4.810.15671440.13942726100
4.81-6.05710.21941630.16662753100
6.0571-41.7880.17591340.1588294699

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