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- PDB-3ll9: X-ray structures of isopentenyl phosphate kinase -

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Basic information

Entry
Database: PDB / ID: 3ll9
TitleX-ray structures of isopentenyl phosphate kinase
ComponentsIsopentenyl phosphate kinase
KeywordsTRANSFERASE / mevalonate biosynthesis isoprenoid
Function / homology
Function and homology information


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid biosynthetic process / kinase activity / ATP binding
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (unknown)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.148 Å
AuthorsHill, C.P. / Schubert, H.L.
CitationJournal: Acs Chem.Biol. / Year: 2010
Title: X-ray structures of isopentenyl phosphate kinase.
Authors: Mabanglo, M.F. / Schubert, H.L. / Chen, M. / Hill, C.P. / Poulter, C.D.
History
DepositionJan 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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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)60,3205
Polymers59,3742
Non-polymers9463
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-26 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.672, 96.360, 72.430
Angle α, β, γ (deg.)90.000, 120.590, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Isopentenyl phosphate kinase /


Mass: 29686.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (unknown)
Gene: MTH47, MTH_47 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus / References: UniProt: O26153
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 12% PEG 6000, 2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 26, 2009
RadiationMonochromator: Verimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 41362 / Num. obs: 38177 / % possible obs: 92.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.157 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.182.50.45927140.93766.2
2.18-2.2630.37537021.04589.4
2.26-2.373.20.338201.193.3
2.37-2.493.50.26739221.13694.6
2.49-2.653.70.22239171.16595.4
2.65-2.853.80.15939641.09896.1
2.85-3.143.80.10939861.24196.8
3.14-3.593.80.08240181.2497.1
3.59-4.523.70.0740381.09196.9
4.52-503.60.06440961.32897.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.92 Å
Translation2.5 Å19.92 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKK
Resolution: 2.148→29.332 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.758 / SU ML: 0.3 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1812 4.97 %5%
Rwork0.205 ---
obs0.208 36455 94.39 %-
all-38610 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.382 Å2 / ksol: 0.421 e/Å3
Displacement parametersBiso max: 104.92 Å2 / Biso mean: 57.626 Å2 / Biso min: 23.84 Å2
Baniso -1Baniso -2Baniso -3
1-11.198 Å20 Å2-11.682 Å2
2---15.83 Å2-0 Å2
3---4.631 Å2
Refinement stepCycle: LAST / Resolution: 2.148→29.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3813 0 60 106 3979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0233976
X-RAY DIFFRACTIONf_angle_d2.0055380
X-RAY DIFFRACTIONf_chiral_restr0.122610
X-RAY DIFFRACTIONf_plane_restr0.01697
X-RAY DIFFRACTIONf_dihedral_angle_d20.7151507
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.148-2.2060.345970.2612304240181
2.206-2.2710.3261480.2342518266691
2.271-2.3440.2711550.212613276893
2.344-2.4280.3031340.2212630276494
2.428-2.5250.2911370.222670280795
2.525-2.640.2981210.2152718283995
2.64-2.7790.2781270.222698282596
2.779-2.9530.2891570.2332729288696
2.953-3.180.3181310.2252726285797
3.18-3.50.2411570.2132724288197
3.5-4.0050.2191410.1692765290697
4.005-5.0420.2151550.1642731288697
5.042-29.3350.261520.2142817296998

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