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- PDB-7lnv: Apo Structure of Isopentenyl Phosphate Kinase from Candidatus met... -

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Basic information

Entry
Database: PDB / ID: 7lnv
TitleApo Structure of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus
ComponentsIsopentenyl phosphate kinase
KeywordsTRANSFERASE / Phosphotransferase ATP Biocatalysis Isoprenoids Enzyme Promiscuity
Function / homology
Function and homology information


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid 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
MALONATE ION / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThomas, L.M. / Singh, S. / Scull, E.M. / Bourne, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus .
Authors: Johnson, B.P. / Kumar, V. / Scull, E.M. / Thomas, L.M. / Bourne, C.R. / Singh, S.
History
DepositionFeb 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9887
Polymers91,6003
Non-polymers3884
Water4,053225
1
B: Isopentenyl phosphate kinase
C: Isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3635
Polymers61,0662
Non-polymers2963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-21 kcal/mol
Surface area21830 Å2
MethodPISA
2
A: Isopentenyl phosphate kinase
hetero molecules

A: Isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2514
Polymers61,0662
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3660 Å2
ΔGint-24 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.392, 45.630, 113.874
Angle α, β, γ (deg.)90.000, 121.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-466-

HOH

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Components

#1: Protein Isopentenyl phosphate kinase / IPK


Mass: 30533.225 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea)
Gene: BKD89_07040 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3G3II74, isopentenyl phosphate kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 0.2 M Sodium Malonate pH 7.0, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 25, 2016 / Details: Osmic Veri Max mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 44070 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.89 Å2 / CC1/2: 0.997 / Χ2: 0.982 / Net I/σ(I): 9.91
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 2159 / CC1/2: 0.552

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-30001.17.1_3660data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKK

3lkk


Resolution: 2.2→37.29 Å / SU ML: 0.3045 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2814 2005 4.55 %
Rwork0.2278 42048 -
obs0.2303 44053 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 26 225 5857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295711
X-RAY DIFFRACTIONf_angle_d0.51977679
X-RAY DIFFRACTIONf_chiral_restr0.0437885
X-RAY DIFFRACTIONf_plane_restr0.0038997
X-RAY DIFFRACTIONf_dihedral_angle_d7.8516801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.34751360.32062880X-RAY DIFFRACTION97.57
2.25-2.310.33181430.2993003X-RAY DIFFRACTION99.59
2.31-2.380.30881410.28292961X-RAY DIFFRACTION99.49
2.38-2.460.33351360.27152965X-RAY DIFFRACTION99.97
2.46-2.550.30051470.26863017X-RAY DIFFRACTION99.97
2.55-2.650.32921370.26722975X-RAY DIFFRACTION100
2.65-2.770.33851470.26462986X-RAY DIFFRACTION99.97
2.77-2.910.32091350.26463010X-RAY DIFFRACTION100
2.91-3.10.32731470.24662982X-RAY DIFFRACTION100
3.1-3.340.24941500.22583023X-RAY DIFFRACTION100
3.34-3.670.26511450.21023015X-RAY DIFFRACTION100
3.67-4.20.25341370.19613039X-RAY DIFFRACTION99.87
4.2-5.290.22061530.18083039X-RAY DIFFRACTION99.87
5.29-37.290.28211510.19863153X-RAY DIFFRACTION99.7

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