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- PDB-3lkk: Crystal structure of the isopentenyl phosphate kinase substrate c... -

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Basic information

Entry
Database: PDB / ID: 3lkk
TitleCrystal structure of the isopentenyl phosphate kinase substrate complex
ComponentsGamma-glutamyl kinase related protein
KeywordsTRANSFERASE / isopentenyl phosphate kinase / alternate mevalonate pathway / alpha-beta-alpha sandwich fold / substrate complex / Kinase
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 / 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'-TRIPHOSPHATE / Isopentenyl phosphate / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsMabanglo, M.F. / Hill, C.P.
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 27, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-glutamyl kinase related protein
B: Gamma-glutamyl kinase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4366
Polymers55,0892
Non-polymers1,3474
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-16 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.307, 44.279, 91.764
Angle α, β, γ (deg.)90.00, 109.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gamma-glutamyl kinase related protein / Isopentenyl phosphate kinase


Mass: 27544.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: topo-cloning reaction was used to insert the Ta0103 gene, and translated protein contained histidine tag, V5 epitope and TEV protease recognition site
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM1728 / Gene: Ta0103 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL / References: UniProt: Q9HLX1
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MIB buffer (2:3:3 molar ratio of sodium malonate, imidazole, boric acid), pH 7.0, 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 274K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2008 / Details: mirrors
RadiationMonochromator: Verimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 31502 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.475 / % possible all: 95.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.3 Å
Translation2.5 Å29.3 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T.acidophilum isopentenyl phosphate kinase solved by single-wavelength anomalous diffraction (SAD)

Resolution: 2.001→29.303 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.28 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1599 5.08 %
Rwork0.1758 --
obs0.1786 31495 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.151 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3025 Å2-0 Å20.7261 Å2
2--0.3082 Å20 Å2
3----2.6107 Å2
Refinement stepCycle: LAST / Resolution: 2.001→29.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 82 198 3926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193798
X-RAY DIFFRACTIONf_angle_d1.7835134
X-RAY DIFFRACTIONf_dihedral_angle_d16.1611436
X-RAY DIFFRACTIONf_chiral_restr0.101569
X-RAY DIFFRACTIONf_plane_restr0.008643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0009-2.06540.28671390.21932573X-RAY DIFFRACTION94
2.0654-2.13920.2591430.19392632X-RAY DIFFRACTION96
2.1392-2.22490.26261330.17222678X-RAY DIFFRACTION97
2.2249-2.32610.20151570.16352673X-RAY DIFFRACTION97
2.3261-2.44870.22771440.1532696X-RAY DIFFRACTION98
2.4487-2.6020.23411280.1742733X-RAY DIFFRACTION98
2.602-2.80280.24261370.17652716X-RAY DIFFRACTION99
2.8028-3.08450.25021460.17612758X-RAY DIFFRACTION99
3.0845-3.53020.24171650.17612761X-RAY DIFFRACTION99
3.5302-4.44520.20871440.15382810X-RAY DIFFRACTION100
4.4452-29.30640.19321630.17142866X-RAY DIFFRACTION100

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