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- PDB-7v2s: Crystal structure of juvenile hormone acid methyltransferase JHAM... -

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Basic information

Entry
Database: PDB / ID: 7v2s
TitleCrystal structure of juvenile hormone acid methyltransferase JHAMT isoform3 from silkworm
ComponentsMethyltranfer_dom domain-containing protein
KeywordsHORMONE / juvenile hormone / methyltransferase / insects
Function / homologyMethyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Methyltranfer_dom domain-containing protein
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.133 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
DepositionAug 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,3772
Polymers68,3772
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-8 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.057, 52.564, 57.261
Angle α, β, γ (deg.)69.007, 75.727, 83.352
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Methyltranfer_dom domain-containing protein / juvenile hormone acid methyltransferase isoform3


Mass: 34188.359 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH8.5, 0.2M magnesium chloride, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.13→52.14 Å / Num. obs: 28167 / % possible obs: 94.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.136 / Net I/σ(I): 17.11
Reflection shellResolution: 2.13→2.22 Å / Rmerge(I) obs: 0.452 / Num. unique obs: 2312

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
MOLREPphasing
PDB_EXTRACT3.27data extraction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.133→52.137 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.193 / SU B: 7.032 / SU ML: 0.177 / Average fsc free: 0.8702 / Average fsc work: 0.8931 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1382 4.906 %RANDOM
Rwork0.1945 26785 --
all0.197 ---
obs-28167 93.893 %-
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: 47.038 Å2
Baniso -1Baniso -2Baniso -3
1-1.638 Å2-2.51 Å20.272 Å2
2--0.867 Å20.506 Å2
3----1.897 Å2
Refinement stepCycle: LAST / Resolution: 2.133→52.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 0 10 4228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134313
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174018
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.6495800
X-RAY DIFFRACTIONr_angle_other_deg1.2541.5839376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4215512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39423.904228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45515768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7441516
X-RAY DIFFRACTIONr_chiral_restr0.070.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
X-RAY DIFFRACTIONr_nbd_refined0.2180.2878
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.23667
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22012
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2104
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.29
X-RAY DIFFRACTIONr_nbd_other0.2330.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.25
X-RAY DIFFRACTIONr_mcbond_it3.5434.6772054
X-RAY DIFFRACTIONr_mcbond_other3.5364.6762053
X-RAY DIFFRACTIONr_mcangle_it5.227.0112564
X-RAY DIFFRACTIONr_mcangle_other5.2227.0122565
X-RAY DIFFRACTIONr_scbond_it4.6785.2672259
X-RAY DIFFRACTIONr_scbond_other4.6775.2662260
X-RAY DIFFRACTIONr_scangle_it7.3017.6423236
X-RAY DIFFRACTIONr_scangle_other7.37.6423237
X-RAY DIFFRACTIONr_lrange_it9.57155.2964670
X-RAY DIFFRACTIONr_lrange_other9.5755.2984671
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
2.133-2.1880.318840.28414780.28622070.7170.76170.77480.268
2.188-2.2480.26860.25817000.25821210.8180.82484.20560.24
2.248-2.3130.318970.26218720.26521710.7750.82290.69550.245
2.313-2.3840.291880.24218280.24420430.8070.8693.78370.219
2.384-2.4620.263810.23217900.23419390.840.86596.4930.213
2.462-2.5480.289990.22917630.23219070.8430.87997.64030.211
2.548-2.6440.273890.22517160.22718460.8740.89397.7790.206
2.644-2.7520.292890.21616790.2218030.8680.89698.05880.203
2.752-2.8740.26970.20615620.2116910.8990.90598.10760.193
2.874-3.0140.235700.20215480.20416400.9220.91598.65850.189
3.014-3.1760.269820.214220.20315350.8980.92397.98050.189
3.176-3.3680.217750.17513690.17714660.9330.94698.49930.173
3.368-3.60.208630.17212940.17413810.9360.95198.26210.172
3.6-3.8870.211670.16811960.1712940.9420.95797.60430.17
3.887-4.2550.224420.15710830.1611640.9390.95896.64950.168
4.255-4.7530.218510.1629900.16510860.9440.95395.85640.177
4.753-5.4810.187370.1628570.1639120.9560.96498.02630.179
5.481-6.6950.282350.2267530.2298130.9170.92496.9250.243
6.695-9.3910.233290.1785800.1816200.9250.94398.22580.2
9.391-52.1370.212210.2153050.2153490.9640.9593.40970.247

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