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- PDB-7veo: Crystal structure of juvenile hormone acid methyltransferase silk... -

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Basic information

Entry
Database: PDB / ID: 7veo
TitleCrystal structure of juvenile hormone acid methyltransferase silkworm JHAMT isoform3 complex with S-Adenosyl-L-homocysteine
ComponentsMethyltranfer_dom domain-containing protein
KeywordsHORMONE / juvenile hormone / methyltransferase / insects
Function / homologyMethyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltranfer_dom domain-containing protein
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsGuo, P.C. / Zhang, Y.S. / Zhang, l. / Xu, H.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970468 China
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2022
Title: Structural characterization and functional analysis of juvenile hormone acid methyltransferase JHAMT3 from the silkworm, Bombyx mori.
Authors: Zhang, L. / Xu, H. / Zhang, Y. / Zhang, H. / Wang, Z. / Guo, P. / Zhao, P.
History
DepositionSep 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,7293
Polymers67,3452
Non-polymers3841
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-10 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.150, 69.170, 57.820
Angle α, β, γ (deg.)90.000, 99.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyltranfer_dom domain-containing protein / juvenile hormone acid methyltransferase like protein


Mass: 33672.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli) / References: UniProt: H9JLJ1
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.15M DL-malic acid pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.53→56.956 Å / Num. obs: 18812 / % possible obs: 96.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.096 / Net I/σ(I): 11.9
Reflection shellResolution: 2.53→2.6 Å / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2 / Num. unique obs: 1399 / Rpim(I) all: 0.524

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V2S

7v2s


Resolution: 2.53→56.956 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.207 / Average fsc free: 0.8789 / Average fsc work: 0.9 / Cross valid method: FREE R-VALUE / ESU R: 1.014 / ESU R Free: 0.305
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2414 904 4.806 %
Rwork0.192 17907 -
all0.195 --
obs-18811 96.314 %
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: 74.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.015 Å2-0 Å20 Å2
2---0.041 Å2-0 Å2
3---0.053 Å2
Refinement stepCycle: LAST / Resolution: 2.53→56.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 26 6 4220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134312
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174118
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.6435802
X-RAY DIFFRACTIONr_angle_other_deg2.2611.5899525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5755508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27723.894226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13415818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4921516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024805
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02986
X-RAY DIFFRACTIONr_nbd_refined0.2020.2842
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.23665
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21997
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.21990
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.210
X-RAY DIFFRACTIONr_nbd_other0.2550.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.21
X-RAY DIFFRACTIONr_mcbond_it5.4017.4112041
X-RAY DIFFRACTIONr_mcbond_other5.3877.4112040
X-RAY DIFFRACTIONr_mcangle_it7.79711.1242546
X-RAY DIFFRACTIONr_mcangle_other7.79811.1242547
X-RAY DIFFRACTIONr_scbond_it6.6618.0972271
X-RAY DIFFRACTIONr_scbond_other6.668.0962271
X-RAY DIFFRACTIONr_scangle_it10.12311.833256
X-RAY DIFFRACTIONr_scangle_other10.12111.8293256
X-RAY DIFFRACTIONr_lrange_it12.81785.1934651
X-RAY DIFFRACTIONr_lrange_other12.81685.1924652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.53-2.5960.336550.31913400.3214310.7620.79497.48430.305
2.596-2.6670.372550.31912980.32114010.790.79796.57390.306
2.667-2.7440.316710.29112420.29213640.8090.83396.2610.263
2.744-2.8280.329610.27812010.2813150.8180.85795.96960.25
2.828-2.920.312570.24610890.24912800.8420.88889.53120.223
2.92-3.0230.326590.22511410.22912270.8420.89997.79950.207
3.023-3.1360.333460.21611160.2211920.8620.90597.48320.207
3.136-3.2640.241550.20210850.20411580.9160.93198.44560.196
3.264-3.4090.249580.19510300.19811020.9140.94398.72960.194
3.409-3.5740.214500.19410100.19510760.9250.93798.5130.195
3.574-3.7670.295520.1989120.2049890.9020.92897.47220.205
3.767-3.9940.23500.1868720.1899530.9150.93196.74710.201
3.994-4.2690.253390.1817540.1858930.9350.9488.80180.202
4.269-4.6090.2360.1517860.1538410.9440.9697.74080.178
4.609-5.0450.204390.1517260.1547740.9480.96398.83720.181
5.045-5.6350.168360.1636600.1637080.9630.96498.30510.203
5.635-6.4960.285300.1785740.1846220.940.94497.10610.213
6.496-7.930.216200.1714760.1735280.9470.95493.93940.213
7.93-11.1080.127190.1483660.1474210.9850.97391.44890.177
11.108-56.9560.328160.2552290.262530.8960.92996.83790.315

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