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- PDB-9xyq: Crystal structure of juvenile hormone acid methyltransferase CfJH... -

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Basic information

Entry
Database: PDB / ID: 9xyq
TitleCrystal structure of juvenile hormone acid methyltransferase CfJHAMT in complex with SAH (crystal form 2)
Componentsjuvenile hormone acid methyltransferase JHAMT
KeywordsBIOSYNTHETIC PROTEIN / juvenile hormone / methyltransferase / SAH / JHAMT
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesChoristoneura fumiferana (eastern spruce budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 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
Revision 1.1Jun 3, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: juvenile hormone acid methyltransferase JHAMT
B: juvenile hormone acid methyltransferase JHAMT
C: juvenile hormone acid methyltransferase JHAMT
D: juvenile hormone acid methyltransferase JHAMT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,48224
Polymers129,3074
Non-polymers2,17420
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, the asymmetric unit contains four chains but this protein is monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.471, 193.835, 34.788
Angle α, β, γ (deg.)90.02, 90.13, 89.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 12 - 273 / Label seq-ID: 15 - 276

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
juvenile hormone acid methyltransferase JHAMT


Mass: 32326.859 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 8.5
Details: 0.2 M Calcium chloride, 0.1 M TRIS pH 8.5, 25 %(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.84→48.46 Å / Num. obs: 22456 / % possible obs: 90 % / Redundancy: 1.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.072 / Rrim(I) all: 0.102 / Χ2: 0.34 / Net I/σ(I): 4.7
Reflection shellResolution: 2.84→2.99 Å / Redundancy: 2 % / Rmerge(I) obs: 0.263 / Num. unique obs: 3372 / CC1/2: 0.874 / Rpim(I) all: 0.263 / Rrim(I) all: 0.372 / Χ2: 0.35

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→48.46 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.598 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21473 1142 5.1 %RANDOM
Rwork0.17945 ---
obs0.18127 21313 89.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.576 Å2
Baniso -1Baniso -2Baniso -3
1--42.15 Å2-1.25 Å2-4.85 Å2
2--42.12 Å2-9.91 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.84→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8177 0 120 18 8315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138477
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177832
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.64411454
X-RAY DIFFRACTIONr_angle_other_deg1.3161.58218140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82722.218478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.516151511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3841556
X-RAY DIFFRACTIONr_chiral_restr0.0760.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029343
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021893
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_it4.7064.3893960
X-RAY DIFFRACTIONr_mcbond_other4.7064.3893960
X-RAY DIFFRACTIONr_mcangle_it7.3396.5774929
X-RAY DIFFRACTIONr_mcangle_other7.3396.5774930
X-RAY DIFFRACTIONr_scbond_it3.9594.574517
X-RAY DIFFRACTIONr_scbond_other3.9594.574517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2586.7726526
X-RAY DIFFRACTIONr_long_range_B_refined13.96282.29833869
X-RAY DIFFRACTIONr_long_range_B_other13.96282.29833868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A77680.11
12B77680.11
21A77450.11
22C77450.11
31A77470.11
32D77470.11
41B76900.12
42C76900.12
51B78710.11
52D78710.11
61C77060.12
62D77060.12
LS refinement shellResolution: 2.84→2.909 Å
RfactorNum. reflection% reflection
Rfree0.252 91 -
Rwork0.148 1557 -
obs--86.92 %

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