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- PDB-8e1t: Asp1 kinase in complex with ADPNP Mg IP7 -

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Basic information

Entry
Database: PDB / ID: 8e1t
TitleAsp1 kinase in complex with ADPNP Mg IP7
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
KeywordsTRANSFERASE / Inositol pyrophosphosphate IPP kinase Fission yeast
Function / homology
Function and homology information


regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity / regulation of mitotic spindle elongation (spindle phase three) / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-pentakisphosphate 1-kinase / inositol heptakisphosphate kinase activity / diphosphoinositol-pentakisphosphate kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity ...regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity / regulation of mitotic spindle elongation (spindle phase three) / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-pentakisphosphate 1-kinase / inositol heptakisphosphate kinase activity / diphosphoinositol-pentakisphosphate kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / inositol phosphate metabolic process / signaling / inositol phosphate biosynthetic process / inositol metabolic process / mitotic spindle assembly / regulation of microtubule cytoskeleton organization / 2 iron, 2 sulfur cluster binding / cytoskeleton / phosphorylation / ATP hydrolysis activity / ATP binding / nucleus / cytosol
Similarity search - Function
Histidine acid phosphatase, VIP1 family / VIP1, N-terminal / Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-I7P / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsGoldgur, Y. / Shuman, S. / Benjamin, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: Mbio / Year: 2022
Title: Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States.
Authors: Benjamin, B. / Goldgur, Y. / Jork, N. / Jessen, H.J. / Schwer, B. / Shuman, S.
History
DepositionAug 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9865
Polymers76,7162
Non-polymers1,2713
Water11,908661
1
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6284
Polymers38,3581
Non-polymers1,2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase


Theoretical massNumber of molelcules
Total (without water)38,3581
Polymers38,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.602, 87.511, 85.988
Angle α, β, γ (deg.)90.000, 94.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase / Cortical actin cytoskeleton protein asp1 / InsP6 and PP-IP5 kinase


Mass: 38357.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: asp1, vip1, SPCC1672.06c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O74429, 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-I7P / (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate / 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate


Mass: 740.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H19O27P7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane (pH 8.1), 0.15 M NaF, and 20% PEG 3,350
Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 138213 / % possible obs: 95.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.27 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Χ2: 1.471 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.71-1.743.70.48332720.7840.2780.561.04787.8
1.74-1.7740.44135590.8250.250.5091.09294.5
1.77-1.8140.36235660.8860.2040.4161.13495.7
1.81-1.844.10.32936280.9080.1840.3781.17796.5
1.84-1.884.10.27736260.9280.1540.3181.24596.7
1.88-1.934.10.22736230.9510.1270.2611.29196.9
1.93-1.9740.19336700.9610.1090.2221.34496.9
1.97-2.0340.15936360.9710.0910.1841.39696.9
2.03-2.093.80.13736030.9760.080.161.49596
2.09-2.153.70.11234440.9840.0660.1311.54490.8
2.15-2.2340.135970.9880.0560.1151.61396.7
2.23-2.324.10.08936710.9910.050.1021.64697.5
2.32-2.4340.08137000.9910.0460.0931.797.9
2.43-2.553.90.06936650.9930.040.081.71297.6
2.55-2.713.90.0636770.9940.0350.0691.66997.6
2.71-2.923.70.0536700.9960.0290.0581.68396.7
2.92-3.223.50.0434960.9960.0240.0471.70292.9
3.22-3.683.90.03437070.9970.020.0391.71997.5
3.68-4.643.80.02937080.9960.0180.0341.6398
4.64-503.70.0337460.9970.0180.0351.60596.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8E1H

8e1h


Resolution: 1.71→47.44 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 3817 2.76 %
Rwork0.1824 134396 -
obs0.1833 138213 92.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.91 Å2 / Biso mean: 25.6469 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 1.71→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 0 72 661 5931
Biso mean--42 34.89 -
Num. residues----647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.730.331180.27324062418077
1.73-1.760.25581520.25814939509191
1.76-1.780.25111460.24434942508893
1.78-1.810.30761450.23294996514194
1.81-1.830.25741350.23115082521794
1.83-1.860.26291530.22265029518294
1.86-1.890.24251350.22125078521395
1.89-1.930.271570.20795062521995
1.93-1.960.22181420.20215047518994
1.96-20.25171300.19125073520394
2-2.040.25661500.18995037518794
2.04-2.080.21971450.18695044518993
2.08-2.130.16631140.18554777489190
2.13-2.190.18971230.18374642476587
2.19-2.240.25021440.18395102524695
2.24-2.310.20431430.18075149529295
2.31-2.390.25491520.18565123527595
2.39-2.470.21751510.18835032518395
2.47-2.570.18731350.18785126526195
2.57-2.690.21591260.18945141526795
2.69-2.830.22461510.18095007515894
2.83-3.010.25831370.18524885502291
3.01-3.240.24311280.17074724485288
3.24-3.560.1871450.16285116526196
3.56-4.080.19441550.15425152530797
4.08-5.140.15661460.14995080522694
5.14-47.440.19451590.19684949510893

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