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- PDB-5bya: Crystal structure of the catalytic domain of human diphosphoinosi... -

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Basic information

Entry
Database: PDB / ID: 5bya
TitleCrystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PCP)2-IP4
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
KeywordsTRANSFERASE / methylenebisphosphonate / Phosphonoacetate / Non-hydrolyzable / Pyrophosphate mimics
Function / homology
Function and homology information


inositol-1,3,4,5,6-pentakisphosphate kinase activity / diphosphoinositol pentakisphosphate kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 5-kinase activity / Synthesis of pyrophosphates in the cytosol / inositol hexakisphosphate kinase activity / inositol phosphate metabolic process / inositol phosphate biosynthetic process ...inositol-1,3,4,5,6-pentakisphosphate kinase activity / diphosphoinositol pentakisphosphate kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 5-kinase activity / Synthesis of pyrophosphates in the cytosol / inositol hexakisphosphate kinase activity / inositol phosphate metabolic process / inositol phosphate biosynthetic process / inositol metabolic process / sensory perception of sound / ATP binding / cytosol
Similarity search - Function
Rossmann fold - #11950 / Histidine acid phosphatase, VIP1 family / VIP1, N-terminal / Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / ATP-grasp fold, B domain ...Rossmann fold - #11950 / Histidine acid phosphatase, VIP1 family / VIP1, N-terminal / Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4WZ / ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsWang, H. / Shears, S.B.
CitationJournal: Chem.Commun.(Camb.) / Year: 2015
Title: Synthetic tools for studying the chemical biology of InsP8.
Authors: Riley, A.M. / Wang, H. / Shears, S.B. / L Potter, B.V.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,48017
Polymers37,5691
Non-polymers1,91116
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.567, 110.400, 41.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / Diphosphoinositol pentakisphosphate kinase 2 / Histidine acid phosphatase domain-containing protein ...Diphosphoinositol pentakisphosphate kinase 2 / Histidine acid phosphatase domain-containing protein 1 / InsP6 and PP-IP5 kinase 2 / VIP1 homolog 2 / hsVIP2


Mass: 37568.891 Da / Num. of mol.: 1 / Fragment: UNP residues 42-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIP5K2, HISPPD1, KIAA0433, VIP2 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express (DE3)
References: UniProt: O43314, inositol-hexakisphosphate 5-kinase, diphosphoinositol-pentakisphosphate 1-kinase

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Non-polymers , 6 types, 461 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-4WZ / {[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)


Mass: 816.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H24O28P8
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 55.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium ...Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight, while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM analog.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2015
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 32965 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rsym value: 0.113 / Net I/σ(I): 15.76
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.42 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3T7A

3t7a


Resolution: 1.9→35.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.622 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2017 6.1 %Equivalent
Rwork0.1413 ---
obs0.1448 30891 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.29 Å2 / Biso mean: 22.557 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å2-0 Å2
2---0.3 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 1.9→35.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 112 445 3107
Biso mean--27.18 35.14 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022762
X-RAY DIFFRACTIONr_angle_refined_deg1.3272.0013751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2645329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37524.252127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46115472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1551517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212074
X-RAY DIFFRACTIONr_mcbond_it1.8341.8741302
X-RAY DIFFRACTIONr_mcangle_it2.5142.7951630
X-RAY DIFFRACTIONr_scbond_it2.2492.1341460
X-RAY DIFFRACTIONr_rigid_bond_restr2.09632762
X-RAY DIFFRACTIONr_sphericity_free33.365107
X-RAY DIFFRACTIONr_sphericity_bonded13.06553047
LS refinement shellResolution: 1.9→1.947 Å
RfactorNum. reflection% reflection
Rfree0.268 137 8.5 %
Rwork0.179 2208 -
obs--98.49 %

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