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- PDB-7ec0: Crystal structure of juvenile hormone acid methyltransferase JHAM... -

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Basic information

Entry
Database: PDB / ID: 7ec0
TitleCrystal structure of juvenile hormone acid methyltransferase JHAMT in complex with S-Adenosyl homocysteine and methyl farnesoate
ComponentsJuvenile hormone acid methyltransferase
KeywordsHORMONE / Juvenile hormone / Methyltransferase / Complex
Function / homologyVaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Methyl farnesoate / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.494 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Juvenile hormone acid methyltransferase
D: Juvenile hormone acid methyltransferase
G: Juvenile hormone acid methyltransferase
J: Juvenile hormone acid methyltransferase
M: Juvenile hormone acid methyltransferase
P: Juvenile hormone acid methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,50316
Polymers204,3296
Non-polymers3,17410
Water43224
1
A: Juvenile hormone acid methyltransferase
D: Juvenile hormone acid methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3796
Polymers68,1102
Non-polymers1,2704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Juvenile hormone acid methyltransferase
P: Juvenile hormone acid methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7444
Polymers68,1102
Non-polymers6352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: Juvenile hormone acid methyltransferase
M: Juvenile hormone acid methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3796
Polymers68,1102
Non-polymers1,2704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.459, 101.203, 103.363
Angle α, β, γ (deg.)90.000, 93.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Juvenile hormone acid methyltransferase


Mass: 34054.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-J10 / Methyl farnesoate / (2E,6E)-Methyl 3,7,11-trimethyldodeca-2,6,10-trienoate


Mass: 250.376 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H26O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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). The sequence contains tag residues MHHHHHHSSGVDLGTENLYFQ.

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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: 2.27 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / 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: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→72.26 Å / Num. obs: 58792 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.062 / Χ2: 0.9 / Net I/σ(I): 18.2
Reflection shellResolution: 2.49→2.63 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 8516 / Rrim(I) all: 0.792 / Χ2: 0.77 / % possible all: 99.1

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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
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EBX

7ebx


Resolution: 2.494→72.26 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / ESU R: 0.934 / ESU R Free: 0.353
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 3103 5.283 %RANDOM
Rwork0.2447 55631 --
all0.247 ---
obs-58734 99.131 %-
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: 68.599 Å2
Baniso -1Baniso -2Baniso -3
1-4.541 Å20 Å2-0.878 Å2
2---1.112 Å20 Å2
3----3.296 Å2
Refinement stepCycle: LAST / Resolution: 2.494→72.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12272 0 220 24 12516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01312768
X-RAY DIFFRACTIONr_bond_other_d0.1810.01711887
X-RAY DIFFRACTIONr_angle_refined_deg1.21.64517196
X-RAY DIFFRACTIONr_angle_other_deg2.4921.58327607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06751466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57522.345725
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88152357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5851574
X-RAY DIFFRACTIONr_chiral_restr0.0490.21616
X-RAY DIFFRACTIONr_gen_planes_refined0.0280.0213977
X-RAY DIFFRACTIONr_gen_planes_other0.0220.022772
X-RAY DIFFRACTIONr_nbd_refined0.1940.22501
X-RAY DIFFRACTIONr_symmetry_nbd_other0.240.211680
X-RAY DIFFRACTIONr_nbtor_refined0.1660.25915
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.26071
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2890.222
X-RAY DIFFRACTIONr_nbd_other0.3490.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.26
X-RAY DIFFRACTIONr_mcbond_it1.8957.3225912
X-RAY DIFFRACTIONr_mcbond_other1.8947.3225911
X-RAY DIFFRACTIONr_mcangle_it3.22510.9797362
X-RAY DIFFRACTIONr_mcangle_other3.22510.9797363
X-RAY DIFFRACTIONr_scbond_it1.3357.4696856
X-RAY DIFFRACTIONr_scbond_other1.3357.476857
X-RAY DIFFRACTIONr_scangle_it2.38111.1229834
X-RAY DIFFRACTIONr_scangle_other2.38111.1229835
X-RAY DIFFRACTIONr_lrange_it4.63182.34213994
X-RAY DIFFRACTIONr_lrange_other4.63182.34713995
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
2.494-2.5580.352190.34640710.34643430.710.71798.77960.334
2.558-2.6280.3622390.33139630.33342440.7320.7699.01040.312
2.628-2.7040.3382730.32938100.32941160.7730.79499.19820.306
2.704-2.7870.3832110.31437870.31840380.7770.81299.00940.288
2.787-2.8790.3252460.29336100.29538790.8310.83899.40710.263
2.879-2.980.3552120.335260.30337670.8120.82799.23020.27
2.98-3.0920.3561600.29534220.29736070.7940.82599.30690.266
3.092-3.2180.3221630.2933330.29235210.8410.84899.290.265
3.218-3.3610.2741390.26531930.26533510.8870.89999.4330.246
3.361-3.5240.3171860.26230110.26632210.8560.88499.25490.248
3.524-3.7150.3121760.24828770.25230720.8720.90199.38150.242
3.715-3.9390.2811610.22927130.23228870.9020.92199.54970.23
3.939-4.210.2861520.22525630.22827310.8810.91499.41410.23
4.21-4.5460.2461390.19523780.19825320.9180.93799.40760.211
4.546-4.9780.2431030.20122240.20323390.9240.93699.4870.225
4.978-5.5630.229830.22420300.22421220.9270.92299.57590.249
5.563-6.4170.3600.25118130.25318810.8710.90899.57470.27
6.417-7.8430.251840.22614980.22715870.9050.9299.68490.256
7.843-11.0280.176650.18311730.18212540.9550.95698.72410.225
11.028-72.260.77320.2826360.2967270.8080.92591.88450.349

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