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- PDB-8u0m: Crystal structure of isopentenyl phosphate kinase from Thermococc... -

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Basic information

Entry
Database: PDB / ID: 8u0m
TitleCrystal structure of isopentenyl phosphate kinase from Thermococcus paralvinellae bound to (E)-2-methylbut-2-en-1-yl monophosphate and ATP
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 / cytoplasm
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / : / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesThermococcus paralvinellae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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

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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)65,1926
Polymers63,9262
Non-polymers1,2674
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-32 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.568, 101.067, 64.735
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-409-

HOH

21B-406-

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 / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-U5O / (2E)-2-methylbut-2-en-1-yl dihydrogen phosphate


Mass: 166.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.133 M magnesium formate, 10.0% 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: 2.54→40 Å / Num. obs: 19727 / % possible obs: 91 % / Redundancy: 5.9 % / Biso Wilson estimate: 56.19 Å2 / CC1/2: 1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Net I/σ(I): 15.8
Reflection shellResolution: 2.54→2.58 Å / Num. unique obs: 503 / CC1/2: 0.484 / Rpim(I) all: 0.229 / Rrim(I) all: 0.601 / % possible all: 47.5

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Processing

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

7lnt


Resolution: 2.54→39.83 Å / SU ML: 0.3419 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.8588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2737 1956 10.02 %
Rwork0.2276 17569 -
obs0.2321 19525 90.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.86 Å2
Refinement stepCycle: LAST / Resolution: 2.54→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 78 18 4020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224062
X-RAY DIFFRACTIONf_angle_d0.51835458
X-RAY DIFFRACTIONf_chiral_restr0.0411617
X-RAY DIFFRACTIONf_plane_restr0.0031678
X-RAY DIFFRACTIONf_dihedral_angle_d6.1549544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.60.3974760.3306737X-RAY DIFFRACTION53.66
2.6-2.670.3414960.3168872X-RAY DIFFRACTION64.66
2.67-2.750.42441140.31791040X-RAY DIFFRACTION76.12
2.75-2.840.34911260.29691187X-RAY DIFFRACTION86.32
2.84-2.940.34511450.29261274X-RAY DIFFRACTION94.41
2.94-3.060.29311480.26761336X-RAY DIFFRACTION97.95
3.06-3.20.32821590.27631339X-RAY DIFFRACTION98.75
3.2-3.370.34571470.26241371X-RAY DIFFRACTION99.48
3.37-3.580.29921520.23831373X-RAY DIFFRACTION99.09
3.58-3.860.27321560.23341365X-RAY DIFFRACTION99.09
3.86-4.240.28341540.20751383X-RAY DIFFRACTION99.68
4.24-4.860.21141530.17841394X-RAY DIFFRACTION99.49
4.86-6.120.2631600.21571413X-RAY DIFFRACTION99.62
6.12-39.830.22611700.20011485X-RAY DIFFRACTION99.4

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