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

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Basic information

Entry
Database: PDB / ID: 7ejb
TitleCrystal structure of juvenile hormone acid methyltransferase JHAMT mutant Q15E
ComponentsJuvenile hormone acid methyltransferase
KeywordsHORMONE / juvenile hormone / methyltransferase / insects
Function / homologyVaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 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: To Be Published
Title: Structural insights into catalytic mechanism of juvenile hormone acid methyltransferase JHAMT
Authors: Guo, P.C. / Zhang, Y.S. / Zhang, l. / Xu, H.Y. / Xia, Q.Y.
History
DepositionApr 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: Juvenile hormone acid methyltransferase


Theoretical massNumber of molelcules
Total (without water)34,0561
Polymers34,0561
Non-polymers00
Water00
1
A: Juvenile hormone acid methyltransferase

A: Juvenile hormone acid methyltransferase


Theoretical massNumber of molelcules
Total (without water)68,1122
Polymers68,1122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Unit cell
Length a, b, c (Å)100.820, 100.820, 70.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Juvenile hormone acid methyltransferase


Mass: 34055.797 Da / Num. of mol.: 1 / Mutation: Q15E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli)
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). Residue Q15E represents mutation. Meanwhile, 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: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.1M Ammonium tartrate dibasic, 0.1M Sodium acetate trihydrate pH 4.6

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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 6M / Detector: PIXEL / Date: Jul 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→54.82 Å / Num. obs: 9668 / % possible obs: 99.6 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.16 / Net I/σ(I): 15.7
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 1.487 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 711

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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: 7EBS

7ebs


Resolution: 2.85→54.82 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.921 / SU B: 20.542 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.329 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2762 488 5.1 %RANDOM
Rwork0.2426 ---
obs0.2442 9165 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.9 Å2 / Biso mean: 100.265 Å2 / Biso min: 65.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å2-0.98 Å20 Å2
2---1.95 Å2-0 Å2
3---6.33 Å2
Refinement stepCycle: final / Resolution: 2.85→54.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 0 0 2141
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132189
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172028
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.6432951
X-RAY DIFFRACTIONr_angle_other_deg1.0431.5824712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8875257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30922.683123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62815410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4041513
X-RAY DIFFRACTIONr_chiral_restr0.040.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 28 -
Rwork0.352 675 -
all-703 -
obs--99.58 %

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