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

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Basic information

Entry
Database: PDB / ID: 5dgh
TitleCrystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCP)-IP5
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
KeywordsTRANSFERASE / TRANSFERASE Inositol diphosphoinositol pentakisphosphate kinase Analog methylenebisphosphonate PPIP5K ATP-grasp Pyrophosphate Diphosphate
Function / homology
Function and homology information


inositol-1,3,4,5,6-pentakisphosphate kinase activity / diphosphoinositol pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-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 / inositol hexakisphosphate 5-kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-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-5A3 / ACETATE ION / 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: 2.1 Å
AuthorsWang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Chemistry / Year: 2016
Title: Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues.
Authors: Hager, A. / Wu, M. / Wang, H. / Brown, N.W. / Shears, S.B. / Veiga, N. / Fiedler, D.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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.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

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)39,42516
Polymers37,5691
Non-polymers1,85615
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.900, 110.340, 41.253
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
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): BL21 Arctic Express (DE3)
References: UniProt: O43314, inositol-hexakisphosphate 5-kinase, diphosphoinositol-pentakisphosphate 1-kinase

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Non-polymers , 6 types, 281 molecules

#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-5A3 / Methylenebisphosphonate inositol pentakisphosphate / {[(R)-hydroxy{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic acid


Mass: 738.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H21O26P7
#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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.8 %
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 AMP-PNP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M ...Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMP-PNP 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. The crystals were soaked under the above stabilizing buffer for three days with 2 mM compound.

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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: Jun 12, 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: 2.1→50 Å / Num. obs: 23365 / % possible obs: 96.8 % / Redundancy: 4.8 % / Rsym value: 0.083 / Net I/σ(I): 16.5
Reflection shellResolution: 2.1→2.35 Å / Redundancy: 3 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.5 / % possible all: 87.2

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Processing

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

3t7a


Resolution: 2.1→29.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.275 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 1429 6.1 %Equivalent and expanded
Rwork0.18671 ---
obs0.18945 21891 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.654 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.1→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 108 266 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022722
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.452.0023681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91724.228123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04715462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5661516
X-RAY DIFFRACTIONr_chiral_restr0.0980.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212017
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_it1.592.2591279
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7913.3761598
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7512.461443
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.32819.7524407
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: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 100 -
Rwork0.219 1425 -
obs--86.5 %

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