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- PDB-8g9e: Crystal structure of the catalytic domain of human diphosphoinosi... -

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Basic information

Entry
Database: PDB / ID: 8g9e
TitleCrystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCF2P)-IP5, an analog of 5-IP7
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
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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-YUT / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 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)1ZIAES080046 United States
CitationJournal: Chemistry / Year: 2023
Title: Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs.
Authors: Hostachy, S. / Wang, H. / Zong, G. / Franke, K. / Riley, A.M. / Schmieder, P. / Potter, B.V.L. / Shears, S.B. / Fiedler, D.
History
DepositionFeb 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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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)38,9718
Polymers37,5691
Non-polymers1,4027
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.082, 109.899, 41.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIP5K2, HISPPD1, KIAA0433, VIP2 / Production host: Escherichia coli (E. coli)
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 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-YUT / {difluoro[(R)-hydroxy{[(1s,2R,3S,4S,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic acid


Mass: 774.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19F2O26P7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP, 2 mM CdCl2, Soaking with 2mM 5-PCF2P-InsP5 under pH 5.2 for 3 days , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 40858 / % possible obs: 99.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.04 / Rrim(I) all: 0.096 / Χ2: 0.884 / Net I/σ(I): 11.3 / Num. measured all: 220730
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.785.10.7920300.6730.3790.8790.81699.5
1.78-1.815.20.65320200.7330.3110.7260.8199.2
1.81-1.855.30.5719970.7940.2690.6320.84899.6
1.85-1.895.20.46620180.8370.2220.5180.83499.3
1.89-1.935.30.37820040.8910.180.420.89599.8
1.93-1.975.20.31420630.9280.1490.3490.86199.6
1.97-2.025.30.26619880.9460.1260.2950.85499.7
2.02-2.075.30.22120380.9560.1050.2460.87399.5
2.07-2.145.30.1920330.9650.090.2110.884100
2.14-2.25.30.15420430.970.0730.1720.89599.9
2.2-2.285.10.12320250.9790.0580.1360.89299.4
2.28-2.384.90.10619000.9770.0520.1190.86493
2.38-2.485.90.10120450.9860.0440.1110.90799.7
2.48-2.6160.08820630.9890.0380.0960.902100
2.61-2.785.90.07520620.9910.0330.0820.925100
2.78-2.995.90.06420690.9920.0280.070.922100
2.99-3.295.80.05720680.9930.0250.0620.954100
3.29-3.775.50.05121180.9940.0230.0570.977100
3.77-4.7550.04720160.9930.0220.0520.89195
4.75-505.50.04722580.9940.0210.0520.84299.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3T9D

3t9d


Resolution: 1.75→38.52 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1752 2023 5 %RANDOM
Rwork0.1241 ---
obs0.1267 38308 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.62 Å2 / Biso mean: 21.625 Å2 / Biso min: 10.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å2-0 Å2
2--1.1 Å20 Å2
3----1.99 Å2
Refinement stepCycle: final / Resolution: 1.75→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 78 369 2997
Biso mean--23.17 37.09 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122701
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162426
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.6743680
X-RAY DIFFRACTIONr_angle_other_deg0.8131.5685678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.725517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73510463
X-RAY DIFFRACTIONr_chiral_restr0.1330.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022997
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02524
X-RAY DIFFRACTIONr_rigid_bond_restr16.19435127
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 139 -
Rwork0.173 2535 -
all-2674 -
obs--89.07 %

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