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- PDB-9xyo: Crystal structure of juvenile hormone acid methyltransferase JHAM... -

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Basic information

Entry
Database: PDB / ID: 9xyo
TitleCrystal structure of juvenile hormone acid methyltransferase JHAMT from Choristoneura fumiferana (CfJHAMT) in complex with SAH (crystal form 1)
Componentsjuvenile hormone acid methyltransferase
KeywordsBIOSYNTHETIC PROTEIN / juvenile hormone / methyltransferase / SAH
Function / homologyIODIDE ION / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesChoristoneura fumiferana (eastern spruce budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPicard, M.-E. / Cusson, M. / Shi, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-06954 Canada
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Molecular insights into juvenile hormone maturation by juvenile hormone acid methyltransferase.
Authors: Picard, M.E. / Cusson, M. / Shi, R.
History
DepositionAug 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: juvenile hormone acid methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7273
Polymers34,2161
Non-polymers5112
Water50428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.925, 39.224, 104.674
Angle α, β, γ (deg.)90.00, 97.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein juvenile hormone acid methyltransferase


Mass: 34215.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Choristoneura fumiferana (eastern spruce budworm)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#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: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 296 K / Method: microbatch / Details: 0.1 M Magnesium formate, 15 %(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.6039 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6039 Å / Relative weight: 1
ReflectionResolution: 2.1→39.22 Å / Num. obs: 15890 / % possible obs: 95.8 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 15.3 / Num. measured all: 104888
Reflection shellResolution: 2.1→2.21 Å / % possible obs: 93.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.768 / Num. measured all: 14315 / Num. unique obs: 2224 / CC1/2: 0.842 / Rpim(I) all: 0.351 / Rrim(I) all: 0.912 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALAdata scaling
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.71 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.628 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25353 739 4.7 %RANDOM
Rwork0.20819 ---
obs0.21036 15142 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.065 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-0 Å20.28 Å2
2---2.97 Å2-0 Å2
3---4.17 Å2
Refinement stepCycle: 1 / Resolution: 2.1→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 27 28 1670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131671
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171530
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.6412258
X-RAY DIFFRACTIONr_angle_other_deg1.4481.583529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26922.26284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.85315279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0911510
X-RAY DIFFRACTIONr_chiral_restr0.080.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021860
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02357
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7323.683831
X-RAY DIFFRACTIONr_mcbond_other2.6293.684831
X-RAY DIFFRACTIONr_mcangle_it3.9155.4941030
X-RAY DIFFRACTIONr_mcangle_other3.9135.4981031
X-RAY DIFFRACTIONr_scbond_it3.4174.085840
X-RAY DIFFRACTIONr_scbond_other3.4154.086840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5085.991229
X-RAY DIFFRACTIONr_long_range_B_refined7.68743.511843
X-RAY DIFFRACTIONr_long_range_B_other7.68843.4691842
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 70 -
Rwork0.324 1041 -
obs--91.74 %
Refinement TLS params.Method: refined / Origin x: 6.1281 Å / Origin y: 0.0096 Å / Origin z: 18.3164 Å
111213212223313233
T0.0302 Å20.0291 Å2-0.0373 Å2-0.2787 Å2-0.0349 Å2--0.4164 Å2
L2.0044 °20.1517 °21.1219 °2-1.9245 °20.5888 °2--2.3992 °2
S-0.0799 Å °-0.4013 Å °0.1246 Å °0.0266 Å °-0.0074 Å °0.0442 Å °0.1605 Å °-0.0795 Å °0.0873 Å °

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