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

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Basic information

Entry
Database: PDB / ID: 7ebx
TitleCrystal structure of juvenile hormone acid methyltransferase JHAMT in complex with S-adenosyl-L-homocysteine.
Componentsjuvenile hormone acid methyltransferase
KeywordsHORMONE / Juvenile hormone / methyltransferase / Comolex / Insects
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsGuo, P.C. / Zhang, Y.S. / Zhang, L. / Xu, H.Y. / Xia, Q.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970468 China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for juvenile hormone biosynthesis by the juvenile hormone acid methyltransferase.
Authors: Guo, P. / Zhang, Y. / Zhang, L. / Xu, H. / Zhang, H. / Wang, Z. / Jiang, Y. / Molloy, D. / Zhao, P. / Xia, Q.
History
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 2, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)31,9682
Polymers31,5831
Non-polymers3841
Water1086
1
A: juvenile hormone acid methyltransferase
hetero molecules

A: juvenile hormone acid methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9354
Polymers63,1662
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/41
Unit cell
Length a, b, c (Å)102.155, 102.155, 102.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein juvenile hormone acid methyltransferase


Mass: 31583.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BMSK0004751.1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


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


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe sequence is corresponding to the entry of KWMTBOMO04857 in Silkbase, or the entry of ...The sequence is corresponding to the entry of KWMTBOMO04857 in Silkbase, or the entry of BMSK0004751.1 in the SilkDB 3.0. It is consist with the partial sequence of XP_037868953.1 (NCBI number, 16-282aa).

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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: 4.22 Å3/Da / Density % sol: 70.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 1M ammonium sulfate, 1% PEG 3350
Temp details: 16

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.89→45.694 Å / Num. obs: 12618 / % possible obs: 100 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 42.867
Reflection shellResolution: 2.89→2.95 Å / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.795 / Num. unique obs: 603 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EBS

7ebs


Resolution: 2.89→45.69 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / ESU R: 0.601 / ESU R Free: 0.366
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2916 645 5.126 %RANDOM
Rwork0.2505 11937 --
all0.253 ---
obs-12582 99.644 %-
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: 112.028 Å2
Baniso -1Baniso -2Baniso -3
1--1.303 Å20 Å20 Å2
2---1.303 Å20 Å2
3---2.605 Å2
Refinement stepCycle: LAST / Resolution: 2.89→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 26 6 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132216
X-RAY DIFFRACTIONr_bond_other_d0.180.0172044
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.6452991
X-RAY DIFFRACTIONr_angle_other_deg2.4891.5834752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04522.602123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96115409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5891513
X-RAY DIFFRACTIONr_chiral_restr0.0440.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.022431
X-RAY DIFFRACTIONr_gen_planes_other0.030.02487
X-RAY DIFFRACTIONr_nbd_refined0.1880.2425
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.21973
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21024
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.21006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.248
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.215
X-RAY DIFFRACTIONr_nbd_other0.2560.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.23
X-RAY DIFFRACTIONr_mcbond_it2.53211.9721031
X-RAY DIFFRACTIONr_mcbond_other2.5311.9721031
X-RAY DIFFRACTIONr_mcangle_it4.53217.9661287
X-RAY DIFFRACTIONr_mcangle_other4.53117.9621288
X-RAY DIFFRACTIONr_scbond_it1.95612.1651184
X-RAY DIFFRACTIONr_scbond_other1.97412.1641184
X-RAY DIFFRACTIONr_scangle_it3.62518.1211703
X-RAY DIFFRACTIONr_scangle_other3.62418.1181704
X-RAY DIFFRACTIONr_lrange_it7.356133.9782435
X-RAY DIFFRACTIONr_lrange_other7.356133.9682436
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
2.89-2.9650.378250.4118240.418840.6730.59796.04070.397
2.965-3.0460.386340.3698520.378860.6710.661000.356
3.046-3.1340.382420.3518190.3538610.7070.7451000.331
3.134-3.2290.341650.337840.3318490.8190.8111000.3
3.229-3.3350.327480.3187540.3198020.8350.8281000.299
3.335-3.4510.324270.3177620.3177890.8490.8281000.296
3.451-3.5810.348360.2917270.2937630.8160.8471000.253
3.581-3.7260.309510.2816890.2837400.8780.8671000.256
3.726-3.890.309430.2636640.2667070.8740.9051000.232
3.89-4.0790.262260.2436630.2436890.90.9221000.212
4.079-4.2980.242420.2176160.2186580.9450.941000.192
4.298-4.5560.256290.2115800.2136090.9310.9421000.191
4.556-4.8670.216330.1965630.1975960.9390.9471000.185
4.867-5.2520.301230.2215020.2245250.9030.9361000.21
5.252-5.7460.265260.2444960.2455220.890.931000.234
5.746-6.4110.404240.274490.2774730.8680.9081000.256
6.411-7.3790.372250.2593940.2664190.8770.9031000.254
7.379-8.9790.228210.1983360.1993570.9470.9571000.205
8.979-12.460.213140.1582800.1612940.9770.981000.178
12.46-45.6940.311110.3731830.3681990.950.90197.48740.388

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