[English] 日本語
Yorodumi
- PDB-8e1s: Asp1 kinase in complex with ADPNP Mn IP6 -

+
Open data


ID or keywords:

Loading...

-
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


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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more