[English] 日本語
Yorodumi
- PDB-7ebs: Crystal structure of juvenile hormone acid methyltransferase JHAM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ebs
TitleCrystal structure of juvenile hormone acid methyltransferase JHAMT from silkworm
ComponentsJuvenile hormone acid methyltransferase
KeywordsHORMONE / juvenile hormone / methyltransferase / insects
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsGuo, P.C. / Zhang, Y.S. / Zhang, L. / Xu, H.Y. / Xia, Q.Y.
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 1.2May 29, 2024Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Juvenile hormone acid methyltransferase


Theoretical massNumber of molelcules
Total (without water)31,5831
Polymers31,5831
Non-polymers00
Water0
1
A: Juvenile hormone acid methyltransferase

A: Juvenile hormone acid methyltransferase


Theoretical massNumber of molelcules
Total (without water)63,1662
Polymers63,1662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444-y-1,-x-1,-z-2/31
Buried area1620 Å2
ΔGint-11 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.584, 99.584, 70.607
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

-
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: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
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).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.59 %
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

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→86.24 Å / Num. obs: 8562 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Net I/σ(I): 30.66
Reflection shellResolution: 2.95→3.06 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 506 / Rrim(I) all: 0.711 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→86.24 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 446 5.2 %RANDOM
Rwork0.2355 ---
obs0.238 8109 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 214.16 Å2 / Biso mean: 103.682 Å2 / Biso min: 64.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å2-0.69 Å2-0 Å2
2---1.37 Å20 Å2
3---4.44 Å2
Refinement stepCycle: final / Resolution: 2.95→86.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 0 0 2140
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132188
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172028
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.6422949
X-RAY DIFFRACTIONr_angle_other_deg2.31.5824712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73322.683123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3281513
X-RAY DIFFRACTIONr_chiral_restr0.0720.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022403
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02480
LS refinement shellResolution: 2.95→3.026 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.263 30 -
Rwork-590 -
obs--97.95 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more