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

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Basic information

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


diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / Synthesis of pyrophosphates in the cytosol / inositol hexakisphosphate kinase activity / inositol phosphate metabolic process ...diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate 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 / phosphorylation / 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-4WY / 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: 2.3 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 1.1Aug 5, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,23913
Polymers37,5691
Non-polymers1,67012
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.807, 110.411, 41.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 41-366
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, 218 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-4WY / {[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(2-oxoethane-2,1-diyl)]}bis(phosphonic acid)


Mass: 744.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O26P6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.81 Å3/Da / Density % sol: 56.24 %
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: 2.3→50 Å / Num. obs: 18773 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.128 / Rsym value: 0.114 / Χ2: 0.921 / Net I/av σ(I): 12.839 / Net I/σ(I): 6 / Num. measured all: 88600
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.344.70.4388650.890.2150.490.84295.5
2.34-2.384.70.428900.8660.2070.470.83896.8
2.38-2.434.60.3789190.9060.1880.4240.83697.8
2.43-2.484.70.3669080.9190.1790.4090.86998.2
2.48-2.534.70.3278980.9250.1610.3660.84498.4
2.53-2.594.60.2919490.9460.1450.3260.83499
2.59-2.664.70.2769130.950.1360.3090.83299.1
2.66-2.734.70.2329250.960.1150.2610.82699.6
2.73-2.814.70.1999290.9740.0980.2230.824100
2.81-2.94.80.1879390.9750.0930.210.836100
2.9-34.80.1559350.9830.0770.1740.845100
3-3.124.80.1369310.9870.0680.1520.922100
3.12-3.264.90.1159510.9890.0570.1290.942100
3.26-3.444.80.19450.9890.050.1121.13799.9
3.44-3.654.80.0929360.990.0460.1031.428100
3.65-3.934.80.0759700.9950.0380.0851.288100
3.93-4.334.80.0579510.9960.0290.0641.022100
4.33-4.954.70.0489730.9970.0240.0540.933100
4.95-6.244.60.059860.9980.0250.0560.823100
6.24-504.30.0310600.9990.0150.0340.63899

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Processing

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

3t7a


Resolution: 2.3→35.57 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.885 / SU B: 6.292 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24638 1143 6.1 %RANDOM
Rwork0.18935 ---
obs0.19287 17585 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.434 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-0 Å2
2---0.32 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 100 206 2845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7382.0113725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10324.228123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63615459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6321516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212025
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7612.1261272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1293.1721585
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7832.2391478
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.81117.7674311
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 76 -
Rwork0.204 1180 -
obs--93.52 %

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