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- PDB-7lnw: I146A mutant of the isopentenyl phosphate kinase from Candidatus ... -

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Basic information

Entry
Database: PDB / ID: 7lnw
TitleI146A mutant of the 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 / 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 / Chem-Y77 / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsThomas, L.M. / Singh, S. / Johnson, B.P.
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 22, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Apr 3, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2816
Polymers60,9822
Non-polymers1,2994
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-31 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.249, 92.998, 52.145
Angle α, β, γ (deg.)90.000, 92.017, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Isopentenyl phosphate kinase / IPK


Mass: 30491.146 Da / Num. of mol.: 2 / Mutation: I146A
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-Y77 / [(~{Z})-5-[(azanylidene-$l^{4}-azanylidene)amino]-3-methyl-pent-2-enyl] dihydrogen phosphate


Mass: 222.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13N3O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.96 Å3/Da / Density % sol: 37.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris pH 5.5 28% w/v PEG 3350, 0.1 M Sodium chloride

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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: Jun 25, 2020 / Details: Omsmic Vari-Max
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.29→30 Å / Num. obs: 21038 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.23 Å2 / Rpim(I) all: 0.074 / Rrim(I) all: 0.155 / Net I/σ(I): 8.86
Reflection shellResolution: 2.29→2.34 Å / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1051 / CC1/2: 0.754 / Rpim(I) all: 0.317 / Rrim(I) all: 0.584

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Solved Native

Resolution: 2.29→28.68 Å / SU ML: 0.2794 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2562 2004 9.55 %
Rwork0.2042 18990 -
obs0.2091 20994 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.24 Å2
Refinement stepCycle: LAST / Resolution: 2.29→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 82 83 3990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193959
X-RAY DIFFRACTIONf_angle_d0.60715331
X-RAY DIFFRACTIONf_chiral_restr0.0433606
X-RAY DIFFRACTIONf_plane_restr0.0033682
X-RAY DIFFRACTIONf_dihedral_angle_d19.469568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.2861410.23371330X-RAY DIFFRACTION96.84
2.35-2.410.311490.23811321X-RAY DIFFRACTION99.86
2.42-2.490.3151360.24511367X-RAY DIFFRACTION99.93
2.49-2.570.26991520.23471351X-RAY DIFFRACTION100
2.57-2.660.31611430.23751332X-RAY DIFFRACTION99.93
2.66-2.760.29131440.22791393X-RAY DIFFRACTION100
2.76-2.890.26941390.23371349X-RAY DIFFRACTION100
2.89-3.040.30491410.23741350X-RAY DIFFRACTION99.87
3.04-3.230.3131420.22861358X-RAY DIFFRACTION99.87
3.23-3.480.22911470.20441371X-RAY DIFFRACTION99.74
3.48-3.830.25171290.18431357X-RAY DIFFRACTION100
3.83-4.380.22321570.18481352X-RAY DIFFRACTION99.15
4.38-5.520.23511420.17281362X-RAY DIFFRACTION99.41
5.52-28.680.18531420.17121397X-RAY DIFFRACTION99.81

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