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- PDB-2if8: Crystal structure of Inositol Phosphate Multikinase Ipk2 in compl... -

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Basic information

Entry
Database: PDB / ID: 2if8
TitleCrystal structure of Inositol Phosphate Multikinase Ipk2 in complex with ADP and Mn2+ 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 tetrakisphosphate 3-kinase activity / Synthesis of pyrophosphates in the cytosol / regulation of arginine metabolic process / inositol-trisphosphate 3-kinase / inositol tetrakisphosphate 6-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate kinase activity ...Synthesis of IPs in the nucleus / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol tetrakisphosphate 3-kinase activity / Synthesis of pyrophosphates in the cytosol / regulation of arginine metabolic process / inositol-trisphosphate 3-kinase / inositol tetrakisphosphate 6-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 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 / phosphorylation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / nucleus / 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
ADENOSINE-5'-DIPHOSPHATE / : / Inositol polyphosphate multikinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 20, 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 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)83,4685
Polymers82,9462
Non-polymers5223
Water6,575365
1
A: Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9954
Polymers41,4731
Non-polymers5223
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)184.996, 184.996, 49.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 100mM HEPES pH7.7, 200mM CaCl2, 28% PEG400 50mM ATP and 50 mM MnCl soaked, 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: Mar 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 36366 / Redundancy: 2.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.6
Reflection shellResolution: 2.398→2.46 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2IEW

2iew


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.249 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24593 1922 5 %RANDOM
Rwork0.19267 ---
obs0.19534 36366 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.898 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20.76 Å20 Å2
2--1.52 Å20 Å2
3----2.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 0 29 365 4568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224281
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9955764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.94624.783207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75715807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0491522
X-RAY DIFFRACTIONr_chiral_restr0.0950.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023169
X-RAY DIFFRACTIONr_nbd_refined0.210.21849
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22861
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2365
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.227
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0280.21
X-RAY DIFFRACTIONr_mcbond_it0.8081.52607
X-RAY DIFFRACTIONr_mcangle_it1.46124094
X-RAY DIFFRACTIONr_scbond_it1.92331900
X-RAY DIFFRACTIONr_scangle_it3.0674.51670
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 141 -
Rwork0.256 2642 -
obs-2642 98.65 %
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)
15.5623.04690.97453.04652.03972.8888-0.0034-0.1012-0.21910.21210.01280.09430.2917-0.3929-0.0094-0.17690.07020.02250.12180.0021-0.087314.841973.602448.0926
21.1718-0.1783-0.13630.9948-0.13582.67990.01070.0115-0.0332-0.0437-0.0393-0.13540.0918-0.13210.0287-0.15240.10230.0061-0.0031-0.017-0.076332.269780.331340.3002
312.27380.907-0.38055.2879-3.09127.25610.2665-1.285-0.99680.4267-0.0594-0.18510.2333-0.0235-0.2072-0.07510.1084-0.10760.13640.0921-0.075836.369970.556359.4565
42.5676-1.5575-0.06598.21781.19453.5230.14430.35180.3741-1.0395-0.0618-0.1888-0.43370.0739-0.08250.1690.22760.0571-0.0790.0805-0.150933.876122.61437.4899
51.9568-0.42770.23664.1385-0.19232.29750.0665-0.01280.05920.2615-0.0323-0.0932-0.2129-0.1154-0.0342-0.01780.17080.033-0.1150.0078-0.163136.2327110.670453.9016
69.19083.5956-2.03766.1864-5.257614.1784-0.15381.09120.4211-0.01360.0981-1.0851-0.28531.47180.0557-0.19880.09430.10750.21430.0720.163955.9293112.943244.5989
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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