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- PDB-7lnu: Ternary complex of the Isopentenyl Phosphate Kinase from Candidat... -

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Basic information

Entry
Database: PDB / ID: 7lnu
TitleTernary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP
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 / phosphorylation / ATP binding
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 / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (unknown)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 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

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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)63,0068
Polymers61,0662
Non-polymers1,9406
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-42 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.892, 74.503, 171.691
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: 30533.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanomethylophilus alvus (unknown)
Gene: BKD89_07040 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3G3II74, isopentenyl phosphate kinase

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Non-polymers , 5 types, 170 molecules

#2: Chemical ChemComp-IP8 / Isopentenyl phosphate / 3-methylbut-3-en-1-yl dihydrogen phosphate


Mass: 166.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 275 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 20, 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: 2.5→50 Å / Num. obs: 18714 / % possible obs: 91 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.42 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.047 / Rrim(I) all: 0.1 / Χ2: 1.024 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.93 / Num. unique obs: 815 / CC1/2: 0.65 / Rpim(I) all: 0.394 / Rrim(I) all: 0.681 / Χ2: 0.925

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-30001.17.1_3660data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: cma apo model

Resolution: 2.5→45.39 Å / SU ML: 0.3092 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.5766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2868 937 5.1 %
Rwork0.2294 17420 -
obs0.2324 18357 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 119 164 4091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213980
X-RAY DIFFRACTIONf_angle_d0.65165374
X-RAY DIFFRACTIONf_chiral_restr0.0454611
X-RAY DIFFRACTIONf_plane_restr0.0028679
X-RAY DIFFRACTIONf_dihedral_angle_d23.2858587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.2991180.24682248X-RAY DIFFRACTION89.83
2.63-2.80.32621100.24532394X-RAY DIFFRACTION94.63
2.8-3.010.33751420.2452469X-RAY DIFFRACTION98.31
3.01-3.320.29461480.24192509X-RAY DIFFRACTION99.66
3.32-3.80.32741520.25922498X-RAY DIFFRACTION97.97
3.8-4.780.21761220.19762570X-RAY DIFFRACTION98.97
4.79-45.390.27111450.20992732X-RAY DIFFRACTION99.93

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