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- PDB-8u0n: Crystal structure of isopentenyl phosphate kinase from Thermococc... -

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Basic information

Entry
Database: PDB / ID: 8u0n
TitleCrystal structure of isopentenyl phosphate kinase from Thermococcus paralvinellae bound to 2-cyclopentylideneethyl 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 / terpenoid biosynthetic process / kinase activity / 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: 2.5 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)65,1646
Polymers63,9262
Non-polymers1,2394
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-35 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.820, 101.064, 64.804
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-408-

HOH

21B-411-

HOH

31B-412-

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-U69 / 2-cyclopentylideneethyl dihydrogen phosphate


Mass: 192.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 50.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 0.113 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: 2.5→38.78 Å / Num. obs: 22665 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 52.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.055 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.996 / Num. unique obs: 2486 / CC1/2: 0.681 / Rpim(I) all: 0.641

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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: 2.5→38.78 Å / SU ML: 0.3656 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.637
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2625 1992 8.81 %
Rwork0.216 20626 -
obs0.2202 22618 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.85 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3873 0 78 21 3972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224011
X-RAY DIFFRACTIONf_angle_d0.62275387
X-RAY DIFFRACTIONf_chiral_restr0.0419611
X-RAY DIFFRACTIONf_plane_restr0.0031667
X-RAY DIFFRACTIONf_dihedral_angle_d9.1578555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.35821450.31071412X-RAY DIFFRACTION98.79
2.56-2.630.35721350.29941440X-RAY DIFFRACTION100
2.63-2.710.35361360.27581477X-RAY DIFFRACTION99.88
2.71-2.80.31761430.26831447X-RAY DIFFRACTION99.81
2.8-2.890.35391420.26441437X-RAY DIFFRACTION99.68
2.9-3.010.33521360.2571457X-RAY DIFFRACTION99.81
3.01-3.150.29721390.23751476X-RAY DIFFRACTION99.94
3.15-3.310.33051430.24551447X-RAY DIFFRACTION100
3.31-3.520.25691410.22131481X-RAY DIFFRACTION99.82
3.52-3.790.25581440.22251474X-RAY DIFFRACTION99.57
3.79-4.170.24881400.20111480X-RAY DIFFRACTION99.94
4.17-4.780.24411460.17191493X-RAY DIFFRACTION99.82
4.78-6.010.20691470.2021519X-RAY DIFFRACTION100
6.02-38.780.22031550.19121586X-RAY DIFFRACTION99.43

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