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

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Basic information

Entry
Database: PDB / ID: 7lnt
TitleTernary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to benzyl 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 / 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 / (phenylmethyl) dihydrogen phosphate / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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
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

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)62,4818
Polymers61,0662
Non-polymers1,4156
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-36 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.698, 74.662, 170.686
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

#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 (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-WZT / (phenylmethyl) dihydrogen phosphate


Mass: 188.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9O4P / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 0.1 M Bis-Tris pH 5.5 15% PEG 10000

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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: Sep 22, 2016 / Details: Osmic Veri Max Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 22277 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 28.17 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.109 / Χ2: 1.037 / Net I/σ(I): 16.9
Reflection shellResolution: 2.35→2.39 Å / Mean I/σ(I) obs: 2.89 / Num. unique obs: 999 / CC1/2: 0.874 / Rpim(I) all: 0.221 / Rrim(I) all: 0.412 / Χ2: 0.712 / % possible all: 89.5

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Processing

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

Resolution: 2.35→29.45 Å / SU ML: 0.2472 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 1072 4.82 %
Rwork0.1871 21151 -
obs0.1894 22223 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.84 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 90 209 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033961
X-RAY DIFFRACTIONf_angle_d0.85655338
X-RAY DIFFRACTIONf_chiral_restr0.0454607
X-RAY DIFFRACTIONf_plane_restr0.0046680
X-RAY DIFFRACTIONf_dihedral_angle_d15.4195574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.460.29691370.22332456X-RAY DIFFRACTION94.6
2.46-2.590.28081160.21952628X-RAY DIFFRACTION98.81
2.59-2.750.29161320.21652625X-RAY DIFFRACTION99.89
2.75-2.960.2861300.21462610X-RAY DIFFRACTION99.46
2.96-3.260.25511290.20222656X-RAY DIFFRACTION99.5
3.26-3.730.23811440.17972662X-RAY DIFFRACTION99.72
3.73-4.70.19341280.15312702X-RAY DIFFRACTION99.86
4.7-29.450.18751560.17612812X-RAY DIFFRACTION99.1

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