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- PDB-4frf: Structural Studies and Protein Engineering of Inositol Phosphate ... -

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Basic information

Entry
Database: PDB / ID: 4frf
TitleStructural Studies and Protein Engineering of Inositol Phosphate Multikinase
ComponentsInositol polyphosphate multikinase alpha
KeywordsTRANSFERASE / ATP Grasp / Inositol phosphate kinase
Function / homology
Function and homology information


pollen germination / pollen tube / pollen tube guidance / inositol-tetrakisphosphate 5-kinase / inositol tetrakisphosphate 5-kinase activity / myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol tetrakisphosphate 3-kinase activity / pollen tube growth ...pollen germination / pollen tube / pollen tube guidance / inositol-tetrakisphosphate 5-kinase / inositol tetrakisphosphate 5-kinase activity / myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol tetrakisphosphate 3-kinase activity / pollen tube growth / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / pollen development / inositol phosphate biosynthetic process / embryo development ending in seed dormancy / kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / D-amino Acid Aminotransferase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Inositol polyphosphate multikinase alpha
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsEndo-Streeter, S.T. / Tsui, M. / Odom, A.R. / York, J.D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural studies and protein engineering of inositol phosphate multikinase.
Authors: Endo-Streeter, S. / Tsui, M.K. / Odom, A.R. / Block, J. / York, J.D.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol polyphosphate multikinase alpha
B: Inositol polyphosphate multikinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0898
Polymers61,5132
Non-polymers5766
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-111 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.790, 130.790, 129.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Inositol polyphosphate multikinase alpha / Inositol polyphosphate 6-/3-/5-kinase alpha / AtIpk2-alpha / AtIpk2alpha


Mass: 30756.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g07370, AtIpmk alpha, IP3K, IPK2a, IPMK, T2I1.80 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9LY23, inositol-tetrakisphosphate 5-kinase, inositol-polyphosphate multikinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

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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: 5.22 Å3/Da / Density % sol: 76.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0M Ammonium sulfate 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→46 Å / Num. all: 28740 / Num. obs: 28740 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.95 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.89→3.06 Å / Redundancy: 10.67 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.25 / Num. unique all: 4348 / % possible all: 93.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.5.0072refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→46 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.919 / SU B: 30.742 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.358 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25099 1420 4.9 %RANDOM
Rwork0.23873 ---
all0.23935 27320 --
obs0.23935 27320 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.945 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 30 0 3474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223550
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.9514793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4515419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10923.765170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38515602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5111518
X-RAY DIFFRACTIONr_chiral_restr0.070.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212654
X-RAY DIFFRACTIONr_mcbond_it0.7891.52113
X-RAY DIFFRACTIONr_mcangle_it1.54423410
X-RAY DIFFRACTIONr_scbond_it2.23831437
X-RAY DIFFRACTIONr_scangle_it3.6884.51383
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 99 -
Rwork0.309 1855 -
obs-1855 100 %
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)
11.9959-0.2394-0.65483.6405-0.77513.28880.1347-0.3559-0.17991.4444-0.26720.76560.5828-1.0740.13241.0525-0.7380.41910.9729-0.10481.0054-52.541.54164.999
21.91290.3728-0.2114.0988-0.51773.7460.0770.046-0.49830.7798-0.33270.26411.0915-0.50780.25560.8848-0.61640.1750.6695-0.07620.8949-43.37835.45256.987
31.9650.00490.18993.7561-0.96743.2262-0.05641.0359-0.189-0.6946-0.21890.08170.8255-0.38430.27540.3778-0.30350.00511.1655-0.11340.7651-40.10748.18125.923
42.6914-0.2206-0.15863.3834-0.73993.6290.02090.86630.3537-0.293-0.21140.2338-0.1401-0.44820.19040.2014-0.2123-0.03571.09570.11030.8083-40.70161.57127.663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 126
2X-RAY DIFFRACTION2A127 - 277
3X-RAY DIFFRACTION3B41 - 126
4X-RAY DIFFRACTION4B127 - 277

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