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- PDB-7pjd: The X-ray structure of juvenile hormone diol kinase from the silk... -

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Basic information

Entry
Database: PDB / ID: 7pjd
TitleThe X-ray structure of juvenile hormone diol kinase from the silk worm Bombyx mori.
ComponentsJuvenile hormone diol kinase
KeywordsMETAL BINDING PROTEIN / EF-hand / calcium binding / kinase / juvenile hormone metabolism. METAL BINDING PROTEIN
Function / homology
Function and homology information


kinase activity / calcium ion binding
Similarity search - Function
EF hand / EF-hand / Recoverin; domain 1 / 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
Juvenile hormone diol kinase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsGuo, J. / Cooper, J. / Keegan, R.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: The X-ray structure of juvenile hormone diol kinase from the silkworm Bombyx mori.
Authors: Guo, J. / Keegan, R.M. / Rigden, D.J. / Erskine, P.T. / Wood, S.P. / Li, S. / Cooper, J.B.
History
DepositionAug 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Juvenile hormone diol kinase
B: Juvenile hormone diol kinase
C: Juvenile hormone diol kinase
D: Juvenile hormone diol kinase
E: Juvenile hormone diol kinase
F: Juvenile hormone diol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,79224
Polymers125,0716
Non-polymers72118
Water8,053447
1
A: Juvenile hormone diol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9654
Polymers20,8451
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Juvenile hormone diol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9654
Polymers20,8451
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Juvenile hormone diol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9654
Polymers20,8451
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Juvenile hormone diol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9654
Polymers20,8451
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Juvenile hormone diol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9654
Polymers20,8451
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Juvenile hormone diol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9654
Polymers20,8451
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.640, 79.430, 100.930
Angle α, β, γ (deg.)90.000, 91.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Juvenile hormone diol kinase


Mass: 20845.182 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: JHDK / Plasmid: pET16b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6URH4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein concentration: 10mg/ml in 0.1 M Bis-Tris pH 5.5 with 25 % (v/v) PEG 3350 as precipitant. The protein was dialysed against 1mM Ca2+ in phosphate-buffered saline before crystallisation.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.99→50.59 Å / Num. obs: 71164 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.99-2.046.91.5933617552370.6450.651.7221.399.9
8.9-50.596.60.02956078480.9990.0120.03149.199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f6t, 4ndd

5f6t

4ndd


Resolution: 1.99→50.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.937 / SU B: 14.517 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 3471 4.9 %RANDOM
Rwork0.1904 ---
obs0.1932 67669 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.58 Å2 / Biso mean: 41.702 Å2 / Biso min: 26.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.73 Å2
2--0.78 Å2-0 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 1.99→50.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8733 0 18 447 9198
Biso mean--39.3 45.23 -
Num. residues----1092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139046
X-RAY DIFFRACTIONr_bond_other_d0.0020.0188259
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.62512260
X-RAY DIFFRACTIONr_angle_other_deg1.4291.59419130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12251109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74125.42476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19151559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0331518
X-RAY DIFFRACTIONr_chiral_restr0.0860.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022070
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 256 -
Rwork0.357 4973 -
all-5229 -
obs--99.92 %
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)
11.5472-0.2127-0.69051.29920.06593.18140.09890.07440.09480.0056-0.12570.0159-0.1341-0.09840.02670.0773-0.0157-0.05550.0368-0.00520.282126.9067-15.285330.7511
22.9957-0.07511.06482.10890.85751.79750.064-0.06630.04210.1048-0.05380.00490.0602-0.0261-0.01020.0803-0.0117-0.03970.00640.02470.2354-5.1481-21.534529.2845
33.03990.87680.3743.56050.77441.29320.1193-0.1222-0.16360.2053-0.1339-0.06450.08590.05240.01460.1244-0.0142-0.01040.03630.04910.2492-2.32511.7993.2141
41.7099-0.6118-0.52832.34270.05712.21630.02430.29970.0274-0.2558-0.04930.1776-0.0582-0.21740.0250.1204-0.0114-0.07290.0997-0.00240.360629.88835.87413.0117
52.22010.31990.96412.2737-0.4811.9813-0.08270.0484-0.19910.1034-0.0716-0.0050.29980.04870.15420.14810.0407-0.00830.0716-0.04240.346815.655925.561836.3422
62.6596-0.1171.84191.86240.11282.5405-0.1338-0.0778-0.06120.0083-0.0261-0.02010.11990.07110.15990.13960.0076-0.01340.0540.02540.325749.250622.723432.6324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 303
2X-RAY DIFFRACTION2B0 - 303
3X-RAY DIFFRACTION3C1 - 303
4X-RAY DIFFRACTION4D1 - 303
5X-RAY DIFFRACTION5E0 - 303
6X-RAY DIFFRACTION6F0 - 303

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