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- PDB-8e1v: Asp1 kinase in complex with ADPNP Mg IP6 -

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Basic information

Entry
Database: PDB / ID: 8e1v
TitleAsp1 kinase in complex with ADPNP Mg IP6
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
KeywordsTRANSFERASE / Inositol pyrophosphosphate IPP kinase Fission yeast
Function / homology
Function and homology information


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 / regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate catabolic process ...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 / regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate catabolic process / inositol phosphate metabolic process / inositol phosphate biosynthetic process / inositol metabolic process / signaling / intracellular phosphate ion homeostasis / mitotic spindle assembly / regulation of microtubule cytoskeleton organization / 2 iron, 2 sulfur cluster binding / cytoskeleton / ATP hydrolysis activity / ATP binding / nucleus / cytosol
Similarity search - Function
Rossmann fold - #11950 / 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 / Rossmann fold ...Rossmann fold - #11950 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / INOSITOL HEXAKISPHOSPHATE / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)77,9065
Polymers76,7162
Non-polymers1,1913
Water8,287460
1
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8883
Polymers38,3581
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0182
Polymers38,3581
Non-polymers6601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.560, 86.990, 86.287
Angle α, β, γ (deg.)90.000, 95.200, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris (pH 5.5), 0.1 M NH4OAc, 17% PEG 10,000.
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: Mar 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 103799 / % possible obs: 98.7 % / Redundancy: 4 % / Biso Wilson estimate: 29.54 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.04 / Rrim(I) all: 0.079 / Χ2: 1.957 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.90.55826680.6430.3340.6530.97499.3
1.93-1.9740.49227500.7480.2890.5731.04198.9
1.97-2.0140.41526900.8260.2430.4831.14198.5
2.01-2.0540.36926680.8440.220.4321.22798.3
2.05-2.093.90.31926650.8610.1910.3741.38598.1
2.09-2.143.70.27426350.8810.1710.3251.47196
2.14-2.193.90.23426930.9130.140.2741.73297.4
2.19-2.254.30.2127450.9460.120.2431.88599.8
2.25-2.324.30.3126900.4920.1810.362.30399.9
2.32-2.394.20.16527500.9640.0950.1912.07599.6
2.39-2.484.10.14527420.970.0850.1692.20799.3
2.48-2.584.10.12427090.9760.0720.1442.37699.4
2.58-2.740.10827020.980.0640.1262.38799.1
2.7-2.843.90.08827410.9850.0530.1042.65399
2.84-3.023.70.07726600.9870.0480.0922.82397.4
3.02-3.253.70.06226940.9920.0370.0732.70997.8
3.25-3.584.20.05327490.9950.030.0622.85899.7
3.58-4.094.20.04427580.9960.0250.0512.55399.5
4.09-5.1640.03527560.9970.0190.042.01599
5.16-504.10.02727900.9990.0150.0311.26398.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8E1H

8e1h


Resolution: 1.9→43.5 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 3825 3.69 %
Rwork0.1971 99974 -
obs0.1981 103799 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.26 Å2 / Biso mean: 34.8339 Å2 / Biso min: 16.03 Å2
Refinement stepCycle: final / Resolution: 1.9→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 68 460 5662
Biso mean--44.28 38.51 -
Num. residues----640
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 (%)
1.9-1.920.34061250.33533388351388
1.92-1.950.34361420.32313713385597
1.95-1.980.34181460.28743783392996
1.98-20.28551400.27553702384296
2-2.030.27111350.26933667380296
2.03-2.070.30481430.25493802394596
2.07-2.10.25591420.24363611375395
2.1-2.140.28781380.23993534367291
2.14-2.180.26631400.23783569370992
2.18-2.220.29731460.22953824397099
2.22-2.260.26471460.21893843398999
2.26-2.310.21981450.22553776392198
2.31-2.370.26791430.21583771391498
2.37-2.420.25081450.21753793393898
2.42-2.490.28041490.21113779392897
2.49-2.560.28481400.21673669380997
2.56-2.650.22081460.20913794394096
2.65-2.740.30131450.21163694383996
2.74-2.850.24151410.20673701384295
2.85-2.980.221390.20663623376293
2.98-3.140.22031300.19993436356689
3.14-3.330.22261450.19023748389397
3.33-3.590.21671440.17463766391097
3.59-3.950.19311450.16913796394197
3.95-4.520.17231360.14813730386697
4.52-5.70.16911390.15893655379495
5.7-43.50.17391500.18113807395798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71970.0501-0.36840.31640.25060.2165-0.1495-0.189-1.13690.2710.0467-0.99690.56110.1653-0.00410.4567-0.0090.00230.27340.05380.643815.1274-34.14317.1456
20.3588-0.2478-0.73430.51250.33931.0499-0.049-0.0044-0.2616-0.11510.1291-0.61260.04450.198300.2140.02880.05450.2175-0.02470.582222.5641-22.13631.7098
30.8109-0.1692-0.27530.880.72731.51110.0413-0.06220.0095-0.0530.0742-0.1726-0.11630.05380.00020.23180.0320.02230.18970.02190.213311.53820.919114.2734
40.7309-0.0106-0.05840.8612-0.41550.60350.0386-0.1653-0.11510.12350.0333-0.0007-0.0524-0.22800.2133-0.0116-0.00290.28080.05330.220.9371-14.908319.8155
51.29070.6934-0.45411.14430.75611.20330.0682-0.027-0.0876-0.075-0.2191-0.0594-0.0358-0.3763-0.01120.2028-0.0024-0.00810.18810.04820.20312.4715-20.20476.6138
61.52540.2224-0.4371.19720.04820.94260.0144-0.00420.1031-0.00750.04530.111-0.17340.038700.2228-0.0183-0.02720.1865-0.00980.162927.5264-24.548838.0486
70.6859-0.1827-0.54790.30850.19860.50680.0354-0.1938-0.2070.07370.051-0.08770.03920.19780.00010.18430.008-0.00870.2394-0.01320.194442.2042-45.70139.5017
80.9081-0.04080.17840.4029-0.03141.59750.00170.0277-0.0397-0.050.1317-0.0543-0.06630.1375-00.1849-0.00230.00890.1895-0.02870.170247.7097-48.811120.8186
90.46770.29030.17970.39680.07430.0434-0.0470.3069-0.0652-0.03890.01190.00380.02730.0405-0.00030.20280.0104-0.0450.3589-0.080.272223.4346-48.076325.9982
101.18950.3359-0.10481.27250.47070.1844-0.05190.1277-0.056-0.04010.0180.1078-0.0066-0.0119-0.00010.1834-0.0009-0.01620.2287-0.03920.212822.4491-42.077934.3878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 68 )A33 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 122 )A69 - 122
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 244 )A123 - 244
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 299 )A245 - 299
5X-RAY DIFFRACTION5chain 'A' and (resid 300 through 362 )A300 - 362
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 122 )B33 - 122
7X-RAY DIFFRACTION7chain 'B' and (resid 123 through 163 )B123 - 163
8X-RAY DIFFRACTION8chain 'B' and (resid 164 through 249 )B164 - 249
9X-RAY DIFFRACTION9chain 'B' and (resid 250 through 299 )B250 - 299
10X-RAY DIFFRACTION10chain 'B' and (resid 300 through 362 )B300 - 362

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