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- PDB-7n9d: I74A mutant of the isopentenyl phosphate kinase from Candidatus m... -

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Basic information

Entry
Database: PDB / ID: 7n9d
TitleI74A 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
(2E)-3-phenylbut-2-en-1-yl dihydrogen phosphate / ADENOSINE-5'-DIPHOSPHATE / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJun 17, 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 1.3Oct 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

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)62,2936
Polymers60,9822
Non-polymers1,3114
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-36 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.293, 172.293, 80.958
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

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Components

#1: Protein Isopentenyl phosphate kinase / IPK


Mass: 30491.146 Da / Num. of mol.: 2 / Mutation: I74A
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-0XI / (2E)-3-phenylbut-2-en-1-yl dihydrogen phosphate


Mass: 228.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5 M Sodium Formate pH 7.0

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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: May 24, 2021 / Details: Osmic Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. obs: 41416 / % possible obs: 99.4 % / Redundancy: 10.8 % / Biso Wilson estimate: 29.46 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 12.32
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 1.189 / Num. unique obs: 1983 / CC1/2: 0.662 / Rsym value: 0.745

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LNV

7lnv


Resolution: 2.1→27.06 Å / SU ML: 0.2916 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2385 3728 4.83 %
Rwork0.2041 73377 -
obs0.2058 41415 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 84 303 4261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244023
X-RAY DIFFRACTIONf_angle_d0.64465430
X-RAY DIFFRACTIONf_chiral_restr0.0448624
X-RAY DIFFRACTIONf_plane_restr0.004693
X-RAY DIFFRACTIONf_dihedral_angle_d12.4894581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.36971240.29582507X-RAY DIFFRACTION90.13
2.13-2.150.3391310.29032601X-RAY DIFFRACTION94.86
2.15-2.180.34911320.28932636X-RAY DIFFRACTION94.09
2.18-2.220.2841320.27442581X-RAY DIFFRACTION94.33
2.22-2.250.35521320.28392626X-RAY DIFFRACTION94.65
2.25-2.280.31141320.26912650X-RAY DIFFRACTION96.46
2.28-2.320.29851340.26222696X-RAY DIFFRACTION96.98
2.32-2.360.28061410.2622728X-RAY DIFFRACTION97.85
2.36-2.40.31871380.24952666X-RAY DIFFRACTION98.11
2.4-2.450.30371360.24942747X-RAY DIFFRACTION98.43
2.45-2.50.2271420.25212733X-RAY DIFFRACTION98.9
2.5-2.550.33591350.2572727X-RAY DIFFRACTION99.24
2.55-2.610.31771410.2512770X-RAY DIFFRACTION99.62
2.61-2.680.30851420.2562748X-RAY DIFFRACTION99.86
2.68-2.750.37821440.24982765X-RAY DIFFRACTION99.9
2.75-2.830.29541450.23632757X-RAY DIFFRACTION99.9
2.83-2.920.30311370.21782782X-RAY DIFFRACTION99.97
2.92-3.030.28911430.21692770X-RAY DIFFRACTION100
3.03-3.150.22391400.21032747X-RAY DIFFRACTION100
3.15-3.290.21011380.19132762X-RAY DIFFRACTION100
3.29-3.470.21821430.1852779X-RAY DIFFRACTION100
3.47-3.680.18521420.17932762X-RAY DIFFRACTION100
3.68-3.970.19391440.15652763X-RAY DIFFRACTION99.86
3.97-4.360.15951400.14942746X-RAY DIFFRACTION99.83
4.36-4.990.15731380.1412769X-RAY DIFFRACTION99.97
4.99-6.280.21571400.17852780X-RAY DIFFRACTION100
6.28-27.060.17471420.17392779X-RAY DIFFRACTION99.93

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