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- PDB-4o4f: Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA ... -

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Basic information

Entry
Database: PDB / ID: 4o4f
TitleCrystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and InsP6
ComponentsInositol hexakisphosphate kinase
KeywordsTRANSFERASE / PDGK Kinase / Inositol Phosphate
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / phosphatidylinositol phosphate biosynthetic process / 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'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / PHOSPHATE ION / Kinase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWang, H. / Shears, S.B.
CitationJournal: Nat Commun / Year: 2014
Title: IP6K structure and the molecular determinants of catalytic specificity in an inositol phosphate kinase family.
Authors: Wang, H. / DeRose, E.F. / London, R.E. / Shears, S.B.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol hexakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7707
Polymers29,3651
Non-polymers1,4066
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.229, 102.229, 109.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-405-

PO4

21A-536-

HOH

31A-686-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inositol hexakisphosphate kinase


Mass: 29364.656 Da / Num. of mol.: 1 / Fragment: UNP residues 27-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI7A_103520 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress (DE3)
References: UniProt: N9UNA8, inositol-hexakisphosphate 5-kinase

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Non-polymers , 5 types, 196 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.4 M NaH2PO4 in the presence of 10 mM ATP,5 mM IP3, 20 mM MgCl2. The crystals were further soaked under 22% (w/v) PEG 3350, 10 mM MgCl2, 10 mM ATP, 0.1 M sodium acetate, pH 5.2, 20 mM IP6 ...Details: 0.4 M NaH2PO4 in the presence of 10 mM ATP,5 mM IP3, 20 mM MgCl2. The crystals were further soaked under 22% (w/v) PEG 3350, 10 mM MgCl2, 10 mM ATP, 0.1 M sodium acetate, pH 5.2, 20 mM IP6 for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 31175 / Num. obs: 31175 / % possible obs: 96.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rsym value: 0.053 / Net I/σ(I): 56.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1145 / Rsym value: 0.54 / % possible all: 71.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4O4C

4o4c


Resolution: 1.7→34.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.522 / SU ML: 0.072 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1568 5 %RANDOM
Rwork0.19129 ---
all0.19277 29589 --
obs0.19277 29589 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.582 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å2-0 Å2
2---0.92 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 79 190 2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192204
X-RAY DIFFRACTIONr_bond_other_d0.0060.022026
X-RAY DIFFRACTIONr_angle_refined_deg1.8252.0092987
X-RAY DIFFRACTIONr_angle_other_deg1.01634708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39624.175103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52515412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1411511
X-RAY DIFFRACTIONr_chiral_restr0.3990.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5632.2121000
X-RAY DIFFRACTIONr_mcbond_other1.5642.209999
X-RAY DIFFRACTIONr_mcangle_it2.5713.3031251
X-RAY DIFFRACTIONr_mcangle_other2.573.3071252
X-RAY DIFFRACTIONr_scbond_it1.8812.5381204
X-RAY DIFFRACTIONr_scbond_other1.8762.5271197
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0773.7211721
X-RAY DIFFRACTIONr_long_range_B_refined6.67219.4892665
X-RAY DIFFRACTIONr_long_range_B_other6.51118.7982583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 81 -
Rwork0.284 1637 -
obs--71.97 %
Refinement TLS params.Method: refined / Origin x: 27.3147 Å / Origin y: -1.0957 Å / Origin z: 12.8057 Å
111213212223313233
T0.0564 Å20.0085 Å20.0183 Å2-0.0175 Å20.028 Å2--0.0627 Å2
L0.9192 °2-0.1923 °20.1582 °2-0.97 °2-0.3045 °2--0.4838 °2
S-0.0361 Å °0.0415 Å °0.0525 Å °0.0096 Å °0.0847 Å °0.1027 Å °-0.0787 Å °-0.0113 Å °-0.0486 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 270
2X-RAY DIFFRACTION1A401 - 404

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