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- PDB-3k52: Crystal Structure of Isopentenyl Phosphate Kinase from M. jannasc... -

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Basic information

Entry
Database: PDB / ID: 3k52
TitleCrystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IP
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 / Amino acid kinase family / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isopentenyl phosphate / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
Model detailsCrystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IP
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 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_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)60,7368
Polymers60,0192
Non-polymers7166
Water1,09961
1


  • Idetical with deposited unit in distinct coordinate
  • defined by author&software
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z1
Buried area4090 Å2
ΔGint-63 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)121,47216
Polymers120,0394
Non-polymers1,43312
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z1
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-143 kcal/mol
Surface area41690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.860, 100.800, 87.320
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 (unknown)
Gene: MJ0044 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60352
#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
#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.: 61 / 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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: crystals were grown in 1.6M ammonium sulfate, transferred to 1.6M ammonium sulfate, 2mM IP, 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: 2.7→50 Å / Num. all: 19488 / Num. obs: 19309 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.88 % / Biso Wilson estimate: 54.186 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.53
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.81 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 10240 / Num. unique all: 3076 / Num. unique obs: 1818 / % possible all: 91.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
BOSdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.65 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.796 / SU B: 13.182 / SU ML: 0.277 / SU R Cruickshank DPI: 1.029 / SU Rfree: 0.377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.029 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.286 983 5.1 %RANDOM
Rwork0.224 ---
obs0.227 19309 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.43 Å2 / Biso mean: 48.71 Å2 / Biso min: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2--1.72 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 40 61 4180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0224205
X-RAY DIFFRACTIONr_angle_refined_deg0.711.9835658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.255511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13125.135185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34115814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5171518
X-RAY DIFFRACTIONr_chiral_restr0.0460.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213058
X-RAY DIFFRACTIONr_mcbond_it0.3661.52539
X-RAY DIFFRACTIONr_mcangle_it0.67124111
X-RAY DIFFRACTIONr_scbond_it0.55331666
X-RAY DIFFRACTIONr_scangle_it0.9644.51547
LS refinement shellResolution: 2.7→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 65 -
Rwork0.315 1233 -
all-1298 -
obs--90.45 %

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