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- PDB-4o4c: Crystal Structure of an Inositol hexakisphosphate kinase apo-EhIP6KA -

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Basic information

Entry
Database: PDB / ID: 4o4c
TitleCrystal Structure of an Inositol hexakisphosphate kinase apo-EhIP6KA
ComponentsInositol hexakisphosphate kinase
KeywordsTRANSFERASE / PDKG 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
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Sep 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol hexakisphosphate kinase
B: Inositol hexakisphosphate kinase


Theoretical massNumber of molelcules
Total (without water)59,7982
Polymers59,7982
Non-polymers00
Water5,909328
1
A: Inositol hexakisphosphate kinase


Theoretical massNumber of molelcules
Total (without water)29,8991
Polymers29,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inositol hexakisphosphate kinase


Theoretical massNumber of molelcules
Total (without water)29,8991
Polymers29,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.418, 128.371, 52.526
Angle α, β, γ (deg.)90.00, 114.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 30 - 270 / Label seq-ID: 15 - 255

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Inositol hexakisphosphate kinase


Mass: 29899.193 Da / Num. of mol.: 2 / Fragment: UNP residues 20-270
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: micro seeding / pH: 5.2
Details: 8% (w/v) PEG 3350, 100 mM Na3Citrate, pH 5.2 at 25C, Micro Seeding, temperature 298K

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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: Jun 28, 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: 1.9→50 Å / Num. obs: 25151 / % possible obs: 98.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.078 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1927 / Rsym value: 0.235 / % possible all: 93.3

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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 4O4B

4o4b


Resolution: 2.2→32.11 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.839 / SU B: 13.702 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28561 1335 5 %RANDOM
Rwork0.22896 ---
all0.23178 25151 --
obs0.23178 25151 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.07 Å2
2--1.14 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 0 328 4348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194136
X-RAY DIFFRACTIONr_bond_other_d0.0030.023921
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9675558
X-RAY DIFFRACTIONr_angle_other_deg0.83339087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64223.98201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58115801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0241522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024538
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02958
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_it1.1841.9061936
X-RAY DIFFRACTIONr_mcbond_other1.1831.9051935
X-RAY DIFFRACTIONr_mcangle_it2.1192.8492420
X-RAY DIFFRACTIONr_mcangle_other2.1192.8512421
X-RAY DIFFRACTIONr_scbond_it0.8852.022200
X-RAY DIFFRACTIONr_scbond_other0.8852.0222201
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5772.9973139
X-RAY DIFFRACTIONr_long_range_B_refined5.46415.8955167
X-RAY DIFFRACTIONr_long_range_B_other5.27815.5295030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15790 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 100 -
Rwork0.243 1795 -
obs--97.53 %
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)
10.7711-0.2549-0.01280.8107-0.05410.1951-0.0084-0.05890.05050.0260.0341-0.0112-0.0527-0.0145-0.02570.0371-0.00640.01990.0289-0.01920.021-2.2821-0.696815.8207
20.9973-0.33160.13650.57270.0280.219-0.0094-0.1001-0.08520.00940.0470.02110.02970.0139-0.03760.0291-0.0108-0.01610.02540.01640.02692.386235.087624.7064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 270
2X-RAY DIFFRACTION2B30 - 270

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