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- PDB-6kth: Crystal structure of Juvenile hormone diol kinase JHDK-L2 from si... -

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Basic information

Entry
Database: PDB / ID: 6kth
TitleCrystal structure of Juvenile hormone diol kinase JHDK-L2 from silkworm, Bombyx mori
ComponentsJuvenile hormone diol kinase
KeywordsHORMONE / kinase / catabolism / EF-hand motif
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsZhang, Y.S. / Xu, H.Y. / Wang, Z. / Zhang, L. / Zhao, P. / Guo, P.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31502019 China
National Natural Science Foundation of China31970468 China
Citation
Journal: Int.J.Biol.Macromol. / Year: 2021
Title: Structural characterization and functional analysis of juvenile hormone diol kinase from the silkworm, Bombyx mori.
Authors: Xu, H. / Zhang, Y. / Zhang, L. / Wang, Z. / Guo, P. / Zhao, P.
#1: Journal: J. Mol. Biol. / Year: 2006
Title: Structure of the neuronal protein calexcitin suggests a mode of interaction in signalling pathways of learning and memory.
Authors: Erskine, P.T. / Beaven, G.D. / Hagan, R. / Findlow, I.S. / Werner, J.M. / Wood, S.P. / Vernon, J. / Giese, K.P. / Fox, G. / Cooper, J.B.
History
DepositionAug 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Juvenile hormone diol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8293
Polymers22,6971
Non-polymers1322
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.960, 67.570, 69.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Juvenile hormone diol kinase


Mass: 22696.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: JHDK-L2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H9JH18
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihyrate pH 5.6, 2 M Ammonium sulfate.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.22→48.484 Å / Num. obs: 67534 / % possible obs: 99.5 % / Redundancy: 12.48 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.6
Reflection shellResolution: 1.22→1.25 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.304 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-3000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CCM

2ccm


Resolution: 1.22→39.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.486 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.04
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2 3427 5.085 %
Rwork0.183 --
obs-67398 99.3 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.451 Å20 Å20 Å2
2---0.031 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.22→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 7 178 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0131556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181353
X-RAY DIFFRACTIONr_angle_refined_deg2.4671.632093
X-RAY DIFFRACTIONr_angle_other_deg1.7161.5933161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01924.9483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86715264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.819153
X-RAY DIFFRACTIONr_chiral_restr0.1420.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02349
X-RAY DIFFRACTIONr_nbd_refined0.2490.2377
X-RAY DIFFRACTIONr_nbd_other0.2320.235
X-RAY DIFFRACTIONr_nbtor_refined0.2030.2810
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.10.25
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_it1.6651.414759
X-RAY DIFFRACTIONr_mcbond_other1.6481.409758
X-RAY DIFFRACTIONr_mcangle_it2.6022.117947
X-RAY DIFFRACTIONr_mcangle_other2.6092.123948
X-RAY DIFFRACTIONr_scbond_it3.4461.711797
X-RAY DIFFRACTIONr_scbond_other3.451.713798
X-RAY DIFFRACTIONr_scangle_it4.9342.4541146
X-RAY DIFFRACTIONr_scangle_other4.9482.4561147
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.22→1.25 Å
RfactorNum. reflection% reflection
Rfree0.493 259 -
Rwork0.46 4647 -
obs--99.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06150.1274-0.00860.2677-0.02820.252-0.00690.0050.0026-0.00750.00880.00030.0052-0.0158-0.00190.0164-0.0032-0.00280.00440.00170.0278-16.0533-9.7086-10.4073
20.2040.1927-0.00740.3382-0.01150.3824-0.00470.0156-0.00730.01350.0109-0.01330.0134-0.0187-0.00610.0119-0.0001-0.00680.00330.00170.0121-17.5816-10.5962-8.6063
300000000000000-00.0447-0.025-0.0110.02620.02560.0337-17.92-8.205-25.292
493.6404-16.9519-25.3662123.8346-84.769372.995-0.20211.08190.5173-1.38230.63670.28991.1017-0.9156-0.43460.032-0.0031-0.02470.025-0.00250.0294-26.7318-8.4017-15.2982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 179
2X-RAY DIFFRACTION2A301 - 478
3X-RAY DIFFRACTION3A201
4X-RAY DIFFRACTION4A202

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