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- PDB-8e1s: Asp1 kinase in complex with ADPNP Mn IP6 -

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Basic information

Entry
Database: PDB / ID: 8e1s
TitleAsp1 kinase in complex with ADPNP Mn IP6
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 / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-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 / 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 / inositol phosphate catabolic process / inositol phosphate metabolic process / inositol phosphate biosynthetic process / signaling / inositol metabolic process / 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
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 / INOSITOL HEXAKISPHOSPHATE / : / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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)77,9926
Polymers76,7162
Non-polymers1,2764
Water13,061725
1
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6345
Polymers38,3581
Non-polymers1,2764
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)48.076, 87.775, 86.048
Angle α, β, γ (deg.)90.000, 94.850, 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-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
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris (pH 5.9), 0.025 M NH4OAc, and 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 16M / 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: 75427 / % possible obs: 97.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 21.99 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.035 / Rrim(I) all: 0.074 / Χ2: 2.181 / Net I/σ(I): 13.4 / Num. measured all: 313795
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.71-1.743.40.63526640.6010.380.7441.27669.8
1.74-1.773.90.59138200.6790.3350.6831.39499.2
1.77-1.814.20.50738260.7760.2780.581.44699.1
1.81-1.844.30.43338400.8560.2330.4931.49299.2
1.84-1.884.40.37337730.8790.20.4251.64599.1
1.88-1.934.40.30638760.9070.1650.3481.76299.2
1.93-1.974.30.25237660.940.1360.2871.91199.3
1.97-2.034.20.21538100.9510.1180.2462.04299
2.03-2.0940.18138570.9590.1020.2092.25299.2
2.09-2.153.80.14537290.9730.0850.1692.33197.5
2.15-2.234.20.1338250.9780.0720.152.699.3
2.23-2.324.40.11738450.9850.0630.1342.63199.4
2.32-2.434.40.10338050.9880.0560.1172.65599.3
2.43-2.554.30.08838550.9890.0480.12.67799.4
2.55-2.714.20.07638420.9920.0420.0872.7899.5
2.71-2.9240.06338290.9930.0360.0732.80899.1
2.92-3.223.80.05137990.9950.030.062.77697.9
3.22-3.684.30.04238550.9970.0220.0482.699.5
3.68-4.644.30.03438730.9980.0190.0392.3399.7
4.64-504.20.02939380.9980.0160.0331.87199.2

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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: 1.72→47.9 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 2028 2.69 %
Rwork0.1761 73364 -
obs0.1769 75392 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.61 Å2 / Biso mean: 27.427 Å2 / Biso min: 12.5 Å2
Refinement stepCycle: final / Resolution: 1.72→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 0 105 725 6028
Biso mean--33.95 35.87 -
Num. residues----647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.760.33731340.30155150528497
1.76-1.810.28611540.24335164531899
1.81-1.860.27771420.21335260540299
1.86-1.920.22791520.19555255540799
1.92-1.990.24231250.19645212533799
1.99-2.070.22121470.18715221536899
2.07-2.160.20331500.17465183533398
2.16-2.270.2071370.16675285542299
2.27-2.420.22721510.17525217536899
2.42-2.60.21471410.17935260540199
2.6-2.870.19181540.17675289544399
2.87-3.280.19211450.17135185533098
3.28-4.130.18231490.152753145463100
4.13-47.90.18661470.16785369551699
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)
10.3908-0.1375-0.12110.2292-0.08740.1838-0.01680.0266-0.58240.21870.0442-0.2760.4108-0.00340.00030.3175-0.01090.04170.22040.01090.345115.3789-34.54365.8939
20.4719-0.001-0.44390.49620.04120.5614-0.0250.05090.0411-0.1770.0583-0.26170.00570.047-00.18430.00820.05050.1651-0.00640.275522.6456-22.07951.2659
30.27220.0781-0.17241.07050.22641.07480.0089-0.0292-0.0137-0.01520.0193-0.0241-0.1129-0.080700.13580.03630.00150.1610.0160.14387.4937-5.270814.597
40.55380.05780.12080.5668-0.11390.3424-0.0431-0.0284-0.1364-0.05310.0390.09960.093-0.21160.00010.1943-0.03120.0150.19620.00520.20923.9194-24.49926.9688
50.74920.1418-0.0561.41590.26550.8781-0.0276-0.04010.12080.01720.0120.0455-0.24190.064900.2167-0.041-0.03730.16580.00720.169128.1939-24.735537.9792
60.5577-0.1298-0.58710.60810.44620.9510.0251-0.0085-0.0333-0.07480.0252-0.0167-0.02030.0573-00.1261-0.0215-0.01920.151-0.00410.144544.7738-48.084226.4658
70.2388-0.0166-0.01110.25260.11640.17890.11330.2053-0.0319-0.10820.0212-0.148-0.3059-0.24760.00460.2078-0.0366-0.02480.2921-0.02010.257519.3005-46.751225.7618
80.73750.350.05550.53270.30240.2979-0.008-0.0318-0.04620.0258-0.0090.10980.0206-0.007900.1453-0.0282-0.01790.1912-0.00370.192423.1562-42.303434.2474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 68 )A31 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 122 )A69 - 122
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 325 )A123 - 325
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 362 )A326 - 362
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 122 )B33 - 122
6X-RAY DIFFRACTION6chain 'B' and (resid 123 through 264 )B123 - 264
7X-RAY DIFFRACTION7chain 'B' and (resid 265 through 299 )B265 - 299
8X-RAY DIFFRACTION8chain 'B' and (resid 300 through 362 )B300 - 362

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