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- PDB-3k4o: Crystal Structure of Isopentenyl Phosphate Kinase from Methanocal... -

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Basic information

Entry
Database: PDB / ID: 3k4o
TitleCrystal Structure of Isopentenyl Phosphate Kinase from Methanocaldococcus jannaschii
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
: / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 5, 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 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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

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)61,09311
Polymers60,0192
Non-polymers1,0749
Water2,756153
1


  • Idetical with deposited unit in distinct coordinate
  • defined by author&software
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z1
Buried area5150 Å2
ΔGint-173 kcal/mol
Surface area21850 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)122,18622
Polymers120,0394
Non-polymers2,14718
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z1
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-368 kcal/mol
Surface area40610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.200, 99.700, 87.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

21A-341-

HOH

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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-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.6M ammonium sulfate, vapor diffusion, hanging drop, temperature 298K

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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: Jul 12, 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→50 Å / Num. all: 45927 / Num. obs: 45753 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.36 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.54
Reflection shellResolution: 2→2.12 Å / Redundancy: 6.36 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.07 / Num. unique all: 7299 / % possible all: 98.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.11phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.831 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.241 2105 4.9 %
Rwork0.223 --
obs-42577 99.9 %
Solvent computationBsol: 64.48 Å2
Displacement parametersBiso max: 103.64 Å2 / Biso mean: 41.29 Å2 / Biso min: 17.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.407 Å20 Å20 Å2
2--1.84 Å20 Å2
3----3.247 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 37 153 4269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5741.5
X-RAY DIFFRACTIONc_scbond_it2.0952
X-RAY DIFFRACTIONc_mcangle_it2.5622
X-RAY DIFFRACTIONc_scangle_it3.1842.5
X-RAY DIFFRACTIONc_angle_deg1.21282
X-RAY DIFFRACTIONc_bond_d0.005547
LS refinement shellResolution: 2.05→2.07 Å
RfactorNum. reflection
Rfree0.3236 47
Rwork0.2864 -
obs-927
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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