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- PDB-9grn: Crystal structure of the engineered C-terminal phosphatase domain... -

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Basic information

Entry
Database: PDB / ID: 9grn
TitleCrystal structure of the engineered C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 (apo, loop deletion residues 848-918)
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
KeywordsBIOSYNTHETIC PROTEIN / Inositol pyrophosphate / inositol pyrophosphate phosphatase / histidine acid phosphatase / phytase / enzyme mechanism / GAF domain / phosphate homeostasis
Function / homology
Function and homology information


inositol hexakisphosphate 4-kinase activity / inositol hexakisphosphate 6-kinase activity / inositol hexakisphosphate 3-kinase activity / regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol / diphosphoinositol pentakisphosphate kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity ...inositol hexakisphosphate 4-kinase activity / inositol hexakisphosphate 6-kinase activity / inositol hexakisphosphate 3-kinase activity / regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol / diphosphoinositol pentakisphosphate kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 5-kinase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / inositol metabolic process / regulation of microtubule cytoskeleton organization / cytoskeleton / ATP binding / cytosol / cytoplasm
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
ACETATE ION / [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsRaia, P. / Lee, K. / Hothorn, M.
Funding support Switzerland, United States, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_209412 Switzerland
Howard Hughes Medical Institute (HHMI)55008733 United States
CitationJournal: Nat Commun / Year: 2025
Title: A small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis.
Authors: Raia, P. / Lee, K. / Bartsch, S.M. / Rico-Resendiz, F. / Portugal-Calisto, D. / Vadas, O. / Panse, V.G. / Fiedler, D. / Hothorn, M.
History
DepositionSep 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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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
C: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
D: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,76142
Polymers234,3434
Non-polymers3,41938
Water84747
1
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,63713
Polymers58,5861
Non-polymers1,05212
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)59,6469
Polymers58,5861
Non-polymers1,0608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,46613
Polymers58,5861
Non-polymers88012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0127
Polymers58,5861
Non-polymers4276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)249.475, 90.516, 200.898
Angle α, β, γ (deg.)90.00, 126.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase / InsP6 and PP-IP5 kinase


Mass: 58585.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VIP1, YLR410W / Cell line (production host): Tnao / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q06685, diphosphoinositol-pentakisphosphate 1-kinase

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Non-polymers , 5 types, 85 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-LPC / [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE


Mass: 468.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H47NO7P
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 % (w/v) polyvinylpyrrolidone K15, 5 mM CoCl2, 0.1M Tris pH 7.0 + 10% additive solution (5mM 13:0 Lyso PC aka 1-tridecanoyl-2-hydroxy-sn-glycero-3-phosphocholine)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 3.4→45.26 Å / Num. obs: 49483 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / CC1/2: 0.98 / Rrim(I) all: 0.463 / Net I/σ(I): 5.3
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 7864 / CC1/2: 0.3 / Rrim(I) all: 2.7 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→45.26 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2945 2472 5 %
Rwork0.2442 --
obs0.2467 49444 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15481 0 198 47 15726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315961
X-RAY DIFFRACTIONf_angle_d0.75821437
X-RAY DIFFRACTIONf_dihedral_angle_d8.8092093
X-RAY DIFFRACTIONf_chiral_restr0.0462338
X-RAY DIFFRACTIONf_plane_restr0.0072719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.460.37421320.35022525X-RAY DIFFRACTION97
3.46-3.530.41121340.33452548X-RAY DIFFRACTION99
3.53-3.610.35071390.32362641X-RAY DIFFRACTION99
3.61-3.690.37671360.30912591X-RAY DIFFRACTION99
3.69-3.790.35641360.30412579X-RAY DIFFRACTION99
3.79-3.890.32511360.29512579X-RAY DIFFRACTION99
3.89-40.35761360.27472592X-RAY DIFFRACTION99
4-4.130.33081370.272601X-RAY DIFFRACTION99
4.13-4.280.31941390.25022631X-RAY DIFFRACTION99
4.28-4.450.30381340.23722561X-RAY DIFFRACTION99
4.45-4.650.2551380.21452612X-RAY DIFFRACTION99
4.65-4.90.23851390.20872638X-RAY DIFFRACTION99
4.9-5.20.27681360.21492583X-RAY DIFFRACTION100
5.2-5.60.29121390.21932641X-RAY DIFFRACTION100
5.6-6.170.2791380.23632627X-RAY DIFFRACTION100
6.17-7.060.30521390.24492639X-RAY DIFFRACTION100
7.06-8.880.25981400.20872656X-RAY DIFFRACTION100
8.88-45.260.23791440.20472728X-RAY DIFFRACTION99
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)
12.64480.52981.62352.26251.09713.9857-0.07390.21270.0895-0.62620.02140.06910.319-0.2588-0.11821.0245-0.03480.14870.66240.06460.3927-56.9902-41.037522.2182
21.6697-0.13250.51393.252-0.19642.96050.40350.3878-0.1265-0.7519-0.3464-0.2383-0.30711.0731-0.16070.79760.08830.35211.0062-0.10520.8582-38.0503-35.748732.4538
35.6075-1.06320.7256.299-0.65344.72380.1154-0.1764-0.5384-0.33280.1726-0.00650.7164-0.1992-0.22940.7272-0.06340.13460.4008-0.07870.5752-62.7268-50.162742.8036
44.3840.56841.27162.38880.30560.77820.1068-0.033-0.0909-0.2454-0.061-0.72610.15970.4614-0.05980.84410.07430.20720.7966-0.02570.6587-36.2686-39.516944.6855
57.45112.41141.11462.21030.56851.37230.4106-0.45910.840.197-0.2720.1353-0.13290.0163-0.05770.59280.04070.21990.7152-0.04260.6946-22.2813-0.814280.4397
60.5251-0.38531.10311.94050.70073.58290.16740.2320.0327-0.1519-0.30850.2338-0.17450.03380.15670.7307-0.0620.28210.7924-0.00270.7032-43.2940.761975.5449
75.6519-2.3811.32693.1173-1.68835.74540.40470.33530.0892-0.3935-0.47420.15170.26480.00770.07180.4661-0.10150.18360.4792-0.04370.84313.83560.127767.2562
82.28151.4684-2.36222.053-0.15964.06230.3379-0.30550.1353-0.07890.04240.4995-0.451-0.0033-0.27950.49660.18180.02570.60330.11420.652128.49638.943866.6347
92.53832.3137-2.22722.267-0.97688.0582-0.1229-0.9163-0.23150.2799-0.5479-0.04880.39971.47740.3660.48020.10570.10930.89860.01280.841226.755-1.204488.3216
104.1671-0.85822.13381.7492-1.86575.6933-0.1263-0.06980.50840.1896-0.2135-0.4428-0.07360.45770.29811.6279-0.04250.29070.6369-0.06340.6236-52.4828-41.6743-15.0827
111.43870.5672-1.2382.27551.12854.11090.05490.1638-0.00450.1226-0.17590.2031-0.6087-0.73410.0951.17850.10390.20870.77570.09020.5125-62.6319-47.9627-27.5308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 538 through 671 )
2X-RAY DIFFRACTION2chain 'A' and (resid 672 through 739 )
3X-RAY DIFFRACTION3chain 'A' and (resid 740 through 925 )
4X-RAY DIFFRACTION4chain 'A' and (resid 926 through 1025 )
5X-RAY DIFFRACTION5chain 'B' and (resid 534 through 671 )
6X-RAY DIFFRACTION6chain 'B' and (resid 672 through 1027 )
7X-RAY DIFFRACTION7chain 'C' and (resid 537 through 700 )
8X-RAY DIFFRACTION8chain 'C' and (resid 701 through 978 )
9X-RAY DIFFRACTION9chain 'C' and (resid 979 through 1023 )
10X-RAY DIFFRACTION10chain 'D' and (resid 542 through 701 )
11X-RAY DIFFRACTION11chain 'D' and (resid 702 through 1089 )

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