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- PDB-2iew: Crystal structure of Inositol Phosphate Multikinase Ipk2 from S. ... -

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Basic information

Entry
Database: PDB / ID: 2iew
TitleCrystal structure of Inositol Phosphate Multikinase Ipk2 from S. cerevisiae
ComponentsInositol polyphosphate multikinase
KeywordsTRANSFERASE / ATP-grasp fold related
Function / homology
Function and homology information


Synthesis of IPs in the nucleus / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / Synthesis of pyrophosphates in the cytosol / regulation of arginine metabolic process / inositol-trisphosphate 3-kinase / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity ...Synthesis of IPs in the nucleus / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / Synthesis of pyrophosphates in the cytosol / regulation of arginine metabolic process / inositol-trisphosphate 3-kinase / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate biosynthetic process / arginine metabolic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / 1-phosphatidylinositol-3-kinase activity / phosphatidylinositol phosphate biosynthetic process / macroautophagy / RNA polymerase II transcription regulator complex / protein-macromolecule adaptor activity / protein stabilization / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / metal ion binding / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHolmes, W. / Jogl, G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of inositol phosphate multikinase 2 and implications for substrate specificity.
Authors: Holmes, W. / Jogl, G.
History
DepositionSep 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
B: Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9863
Polymers82,9462
Non-polymers401
Water8,485471
1
A: Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5132
Polymers41,4731
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol polyphosphate multikinase


Theoretical massNumber of molelcules
Total (without water)41,4731
Polymers41,4731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.510, 186.510, 50.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe asu contains two independent monomers.

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Components

#1: Protein Inositol polyphosphate multikinase / IPMK / Arginine metabolism regulation protein III


Mass: 41473.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IPK2 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star
References: UniProt: P07250, inositol-polyphosphate multikinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 100mM HEPES pH7.7, 200mM CaCl2, 28% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 58988 / Redundancy: 4.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.3
Reflection shellResolution: 1.998→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.371 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25293 4868 7.6 %RANDOM
Rwork0.20775 ---
obs0.21123 58988 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.389 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 1 471 4676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224285
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9835764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11224.714210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26215810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3321522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023188
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21917
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22894
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2425
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0220.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8581.52631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49724118
X-RAY DIFFRACTIONr_scbond_it1.89931873
X-RAY DIFFRACTIONr_scangle_it2.9384.51646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 316 -
Rwork0.279 3890 -
obs-3890 85.11 %
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)
11.72310.74430.53550.58320.51030.82910.0179-0.0458-0.15080.0334-0.0107-0.05910.0381-0.2725-0.0071-0.11710.02270.00780.1574-0.0038-0.03614.595374.233948.1523
20.38850.0365-0.1110.3545-0.11420.72610.0247-0.0001-0.0247-0.0299-0.0537-0.07460.029-0.06510.029-0.06820.07070.00110.0503-0.0036-0.034432.346680.557740.4509
35.80351.7224-1.29133.3774-2.58883.15160.0824-0.4625-0.38460.19810.0128-0.16420.0160.0185-0.0952-0.06170.0588-0.06520.06890.0727-0.023336.076670.416259.3852
41.2591-0.904-0.20554.3992-0.08661.11420.13690.08440.2084-0.7195-0.1154-0.051-0.196-0.0769-0.02150.17020.17170.0555-0.06890.0525-0.077333.6436123.005837.429
50.3769-0.27910.0411.7376-0.17090.87460.03910.0270.02870.1308-0.0597-0.1234-0.1085-0.11210.02060.03580.10990.0224-0.04820.0064-0.057136.3608111.270253.9611
64.38241.5417-0.22935.3059-4.57898.27250.27980.33690.2247-0.197-0.5301-0.93290.07490.890.2503-0.14250.12020.15170.02910.09970.215155.9201113.702344.3153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 11826 - 118
2X-RAY DIFFRACTION2AA127 - 134127 - 134
3X-RAY DIFFRACTION2AA165 - 355165 - 355
4X-RAY DIFFRACTION3AA135 - 164135 - 164
5X-RAY DIFFRACTION4BB26 - 11826 - 118
6X-RAY DIFFRACTION5BB127 - 134127 - 134
7X-RAY DIFFRACTION5BB165 - 355165 - 355
8X-RAY DIFFRACTION6BB135 - 164135 - 164

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