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- PDB-4q4d: Crystal structure of the catalytic domain of human diphosphoinosi... -

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Basic information

Entry
Database: PDB / ID: 4q4d
TitleCrystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and synthetic 3,5-(PP)2-IP4 (3,5-IP8)
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
KeywordsTRANSFERASE / kinase / synthesis / inositol pyrophosphate / enantiomer
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 / inositol hexakisphosphate kinase activity / Synthesis of pyrophosphates in the cytosol / 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 / inositol hexakisphosphate kinase activity / Synthesis of pyrophosphates in the cytosol / 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-2YN / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsWang, H. / Shears, S.B.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Synthesis of Densely Phosphorylated Bis-1,5-Diphospho-myo-Inositol Tetrakisphosphate and its Enantiomer by Bidirectional P-Anhydride Formation.
Authors: Capolicchio, S. / Wang, H. / Thakor, D.T. / Shears, S.B. / Jessen, H.J.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9686
Polymers37,5691
Non-polymers1,3995
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.790, 110.681, 41.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: kinase domain (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): ArcticExpress (DE3)
References: UniProt: O43314, inositol-hexakisphosphate 5-kinase, diphosphoinositol-pentakisphosphate 1-kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-2YN / (1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]


Mass: 819.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H20O30P8
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% w/v PEG3350, 20 mM magnesium chloride, 0.1 M HEPES, pH 7.0, 1 mM AMP-PNP, 2 mM cadmium chloride, crystals transferred to stabilizing buffer (22% w/v PEG3350, 10 mM magnesium chloride, 0. ...Details: 12% w/v PEG3350, 20 mM magnesium chloride, 0.1 M HEPES, pH 7.0, 1 mM AMP-PNP, 2 mM cadmium chloride, crystals transferred to stabilizing buffer (22% w/v PEG3350, 10 mM magnesium chloride, 0.1 M sodium acetate, pH 5.2) at 277 K overnight (ATP in the crystals was hydrolyzed to ADP) then soaked for three days in stabilizing buffer containing 2 mM 3,5-IP8, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2014
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: 1.85→50 Å / Num. all: 35810 / Num. obs: 35810 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.07 / Net I/σ(I): 25.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.366 / % possible all: 96.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3T9F

3t9f


Resolution: 1.85→47.01 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.662 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21584 2197 6.2 %EQUIVALENT AND EXPANDED RANDOM
Rwork0.17968 ---
all0.1819 33431 --
obs0.1819 33431 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.001 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0 Å2
2---0.23 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 78 403 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022747
X-RAY DIFFRACTIONr_bond_other_d0.0010.022556
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9973748
X-RAY DIFFRACTIONr_angle_other_deg0.753.0025911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5315331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62524.048126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0815472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2381518
X-RAY DIFFRACTIONr_chiral_restr0.10.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
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_it1.0031.2181306
X-RAY DIFFRACTIONr_mcbond_other1.0021.2161304
X-RAY DIFFRACTIONr_mcangle_it1.6881.821643
X-RAY DIFFRACTIONr_mcangle_other1.6881.8211644
X-RAY DIFFRACTIONr_scbond_it1.5111.4831441
X-RAY DIFFRACTIONr_scbond_other1.5031.4681433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4452.1442093
X-RAY DIFFRACTIONr_long_range_B_refined6.68612.1973455
X-RAY DIFFRACTIONr_long_range_B_other6.28610.9943229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 165 -
Rwork0.234 2295 -
obs--94.69 %
Refinement TLS params.Method: refined / Origin x: -0.3561 Å / Origin y: 15.2105 Å / Origin z: 3.6185 Å
111213212223313233
T0.0133 Å2-0.0056 Å20.0007 Å2-0.0107 Å2-0.0019 Å2--0.0072 Å2
L0.4805 °2-0.2732 °20.0826 °2-0.7468 °2-0.2915 °2--0.6506 °2
S0.0151 Å °0.0082 Å °-0.0111 Å °-0.0073 Å °0.022 Å °0.0579 Å °0.0272 Å °-0.0184 Å °-0.0371 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 359
2X-RAY DIFFRACTION1A401 - 405

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