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

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Basic information

Entry
Database: PDB / ID: 7lnx
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 / 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
ADENOSINE-5'-DIPHOSPHATE / (2E)-3-methylhept-2-en-1-yl dihydrogen phosphate / Chem-Y7D / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,4257
Polymers60,9822
Non-polymers1,4435
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-33 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.565, 73.277, 166.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isopentenyl phosphate kinase / IPK


Mass: 30491.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: I146A
Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea)
Gene: BKD89_07040 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3G3II74, isopentenyl phosphate kinase

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Non-polymers , 5 types, 59 molecules

#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-Y7D / (2Z)-3-methylhept-2-en-1-yl trihydrogen diphosphate


Mass: 288.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-WOG / (2E)-3-methylhept-2-en-1-yl dihydrogen phosphate


Mass: 208.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17O4P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris pH 5.5 28% PEG 3350. 0.1 M Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→39.42 Å / Num. obs: 22800 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 35.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Rrim(I) all: 0.13 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2038 / CC1/2: 0.71 / Rpim(I) all: 0.531 / Rrim(I) all: 0.877 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.42 Å / SU ML: 0.3594 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.7721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3107 2000 8.8 %
Rwork0.2513 20731 -
obs0.2565 22731 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3669 0 90 54 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00153809
X-RAY DIFFRACTIONf_angle_d0.53435129
X-RAY DIFFRACTIONf_chiral_restr0.0417578
X-RAY DIFFRACTIONf_plane_restr0.003654
X-RAY DIFFRACTIONf_dihedral_angle_d14.8095558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.42121260.32331312X-RAY DIFFRACTION89.54
2.36-2.420.39161370.32091420X-RAY DIFFRACTION97.01
2.42-2.490.37421430.30571478X-RAY DIFFRACTION99.45
2.49-2.570.33641410.3071457X-RAY DIFFRACTION99.75
2.57-2.660.4041420.29921475X-RAY DIFFRACTION99.88
2.66-2.770.34851420.28821470X-RAY DIFFRACTION99.94
2.77-2.90.38221440.28661498X-RAY DIFFRACTION99.82
2.9-3.050.36571420.27441468X-RAY DIFFRACTION99.75
3.05-3.240.32521420.27921480X-RAY DIFFRACTION99.82
3.24-3.490.33541450.26461500X-RAY DIFFRACTION99.76
3.49-3.840.28171450.22691502X-RAY DIFFRACTION100
3.84-4.390.2681470.21551515X-RAY DIFFRACTION99.7
4.39-5.530.26121480.20731536X-RAY DIFFRACTION99.7
5.54-39.420.26791560.2311620X-RAY DIFFRACTION98.83

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