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- PDB-3uds: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in... -

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Basic information

Entry
Database: PDB / ID: 3uds
TitleInositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP.
ComponentsInositol-pentakisphosphate 2-kinase
KeywordsTRANSFERASE / inositol / ipk / ins5p 2-k / atipk1 / ip5 2-k / polyphosphate kinase
Function / homology
Function and homology information


inositol tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium ...inositol tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium / phosphorylation / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Inositol-pentakisphosphate 2-kinase, N-lobe / Inositol-pentakisphosphate 2-kinase / Inositol-pentakisphosphate 2-kinase, N-terminal lobe / Inositol-pentakisphosphate 2-kinase / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGosein, V. / Leung, T.-F. / Krajden, O. / Miller, G.J.
CitationJournal: Protein Sci. / Year: 2012
Title: Inositol phosphate-induced stabilization of inositol 1,3,4,5,6-pentakisphosphate 2-kinase and its role in substrate specificity.
Authors: Gosein, V. / Leung, T.F. / Krajden, O. / Miller, G.J.
History
DepositionOct 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Feb 28, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _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: Inositol-pentakisphosphate 2-kinase
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5666
Polymers110,6632
Non-polymers9034
Water00
1
A: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7833
Polymers55,3321
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7833
Polymers55,3321
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.289, 59.877, 82.913
Angle α, β, γ (deg.)83.400, 89.400, 65.300
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Inositol-pentakisphosphate 2-kinase / Inositol-1 / 3 / 4 / 5 / 6-pentakisphosphate 2-kinase / Ins(1 / 3 / 4 / 5 / 6)P5 2-kinase / AtIPK1 ...Inositol-1 / 3 / 4 / 5 / 6-pentakisphosphate 2-kinase / Ins(1 / 3 / 4 / 5 / 6)P5 2-kinase / AtIPK1 / InsP5 2-kinase


Mass: 55331.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g42810, IPK1, MJB21.19 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: Q93YN9, inositol-pentakisphosphate 2-kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris-HCl, 0.18M CaCl2, 18% PEG6000, 0.01M TCEP, Protein: 10mg/mL, Temp: 293K, pH 8.0, vapor diffusion

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 31, 2010 / Details: VariMax HF
RadiationMonochromator: Confocal dual reflection mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 27584 / Biso Wilson estimate: 62.35 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.3_473refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→42.82 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7105 / SU ML: 0.45 / σ(F): 0.03 / Phase error: 35.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3119 876 5.02 %
Rwork0.237 --
obs0.2408 17449 95.15 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.262 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso max: 143.48 Å2 / Biso mean: 64.3757 Å2 / Biso min: 23.35 Å2
Baniso -1Baniso -2Baniso -3
1-4.3405 Å2-0.4459 Å2-0.969 Å2
2---6.4525 Å2-17.2871 Å2
3---2.112 Å2
Refinement stepCycle: LAST / Resolution: 3.1→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 0 56 0 5796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135904
X-RAY DIFFRACTIONf_angle_d1.3197958
X-RAY DIFFRACTIONf_chiral_restr0.082898
X-RAY DIFFRACTIONf_plane_restr0.005991
X-RAY DIFFRACTIONf_dihedral_angle_d19.3262219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.29420.36581300.25862634276490
3.2942-3.54850.34381490.23392722287194
3.5485-3.90530.2981290.22412800292996
3.9053-4.46990.29681490.19092740288995
4.4699-5.62960.2711550.21642820297598
5.6296-42.82370.3311640.28162857302199

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