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- PDB-8u0l: Crystal structure of isopentenyl phosphate kinase from Thermococc... -

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Basic information

Entry
Database: PDB / ID: 8u0l
TitleCrystal structure of isopentenyl phosphate kinase from Thermococcus paralvinellae bound to (E)-But-2-en-1-yl monophosphate and ADP
ComponentsIsopentenyl phosphate kinase
KeywordsTRANSFERASE / Alternate Mevalonate pathway IPK Amino acid kinase isoprenoids
Function / homology
Function and homology information


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid biosynthetic process / kinase activity / phosphorylation / ATP binding / cytosol
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesThermococcus paralvinellae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSingh, S. / Thomas, L.M. / Johnson, B.P. / Brown, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138800 United States
CitationJournal: Proteins / Year: 2024
Title: Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity.
Authors: Johnson, B.P. / Mandal, P.S. / Brown, S.M. / Thomas, L.M. / Singh, S.
History
DepositionAug 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isopentenyl phosphate kinase
B: Isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0846
Polymers63,9262
Non-polymers1,1594
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-35 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.601, 101.109, 64.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

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Components

#1: Protein Isopentenyl phosphate kinase


Mass: 31962.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus paralvinellae (archaea) / Gene: TES1_0236 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 / References: UniProt: W0I5G2
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-U4R / (2E)-but-2-en-1-yl dihydrogen phosphate


Mass: 152.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.13 M magnesium formate, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→38.76 Å / Num. obs: 15975 / % possible obs: 98.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 65.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.083 / Net I/σ(I): 9.3
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 1.006 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2060 / CC1/2: 0.527 / Rpim(I) all: 0.783

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7LNT

7lnt


Resolution: 2.8→38.76 Å / SU ML: 0.459 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2868 1589 9.97 %
Rwork0.2361 14348 -
obs0.2413 15937 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.6 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 72 4 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273992
X-RAY DIFFRACTIONf_angle_d0.63395360
X-RAY DIFFRACTIONf_chiral_restr0.0424607
X-RAY DIFFRACTIONf_plane_restr0.0038665
X-RAY DIFFRACTIONf_dihedral_angle_d9.1391542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.42631220.35681092X-RAY DIFFRACTION84.13
2.89-2.990.41221340.34861257X-RAY DIFFRACTION95.21
2.99-3.110.35411490.31351295X-RAY DIFFRACTION99.38
3.11-3.250.35851400.28851315X-RAY DIFFRACTION99.73
3.25-3.420.361510.25091320X-RAY DIFFRACTION99.93
3.42-3.640.33541410.26181299X-RAY DIFFRACTION99.52
3.64-3.920.28911480.23811315X-RAY DIFFRACTION100
3.92-4.310.26061480.21731335X-RAY DIFFRACTION99.87
4.31-4.940.24041470.18841329X-RAY DIFFRACTION99.46
4.94-6.210.23481520.22641356X-RAY DIFFRACTION99.54
6.22-38.760.26211570.20911435X-RAY DIFFRACTION99.31

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