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- PDB-3k4y: Crystal Structure of Isopentenyl Phosphate Kinase from M. jannasc... -

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Basic information

Entry
Database: PDB / ID: 3k4y
TitleCrystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IPP
Componentsisopentenyl phosphate kinase
KeywordsTRANSFERASE / small molecule kinase / ATP-binding / Methanocaldococcus jannaschii / isopentenyl monophosphate / isopentenyl diphosphate / isoprenoid biosynthesis / mevalonate pathway / archaea
Function / homology
Function and homology information


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid biosynthetic process / kinase activity / phosphorylation / ATP binding / cytosol
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Glutamate/acetylglutamate kinase / 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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / CNS rigid body / Resolution: 2.54 Å
AuthorsDellas, N. / Noel, J.P.
CitationJournal: Acs Chem.Biol. / Year: 2010
Title: Mutation of archaeal isopentenyl phosphate kinase highlights mechanism and guides phosphorylation of additional isoprenoid monophosphates.
Authors: Dellas, N. / Noel, J.P.
History
DepositionOct 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: isopentenyl phosphate kinase
B: isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8968
Polymers60,0192
Non-polymers8766
Water1,72996
1


  • Idetical with deposited unit in distinct coordinate
  • defined by author&software
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z1
Buried area5010 Å2
ΔGint-70 kcal/mol
Surface area22250 Å2
MethodPISA
2
A: isopentenyl phosphate kinase
B: isopentenyl phosphate kinase
hetero molecules

A: isopentenyl phosphate kinase
B: isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,79216
Polymers120,0394
Non-polymers1,75312
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z1
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-153 kcal/mol
Surface area41650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.090, 99.230, 87.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein isopentenyl phosphate kinase /


Mass: 30009.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0044 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60352
#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: crystals were grown in 1.6M ammonium sulfate and then transferred to a solution containing 1.6M ammonium sulfate, 10mM IPP, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2008
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. all: 22954 / Num. obs: 22723 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.87 % / Biso Wilson estimate: 47.429 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.32
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 5.66 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.5 / Num. measured obs: 12156 / Num. unique all: 3643 / Num. unique obs: 2215 / % possible all: 89.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
BOSdata collection
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: CNS rigid body / Resolution: 2.54→43.71 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.283 / WRfactor Rwork: 0.218 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.777 / SU B: 11.679 / SU ML: 0.256 / SU R Cruickshank DPI: 0.559 / SU Rfree: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.559 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1145 5 %RANDOM
Rwork0.224 ---
obs0.227 22723 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.29 Å2 / Biso mean: 42.056 Å2 / Biso min: 14.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--1.44 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.54→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 48 96 4218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224212
X-RAY DIFFRACTIONr_angle_refined_deg0.7841.9935674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6315505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69725.135185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72815810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7491518
X-RAY DIFFRACTIONr_chiral_restr0.0540.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213050
X-RAY DIFFRACTIONr_mcbond_it0.4481.52515
X-RAY DIFFRACTIONr_mcangle_it0.82824072
X-RAY DIFFRACTIONr_scbond_it0.77131697
X-RAY DIFFRACTIONr_scangle_it1.3334.51602
LS refinement shellResolution: 2.543→2.609 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 74 -
Rwork0.334 1430 -
all-1504 -
obs--90.49 %

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