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- PDB-4axf: InsP5 2-K in complex with Ins(3,4,5,6)P4 plus AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4axf
TitleInsP5 2-K in complex with Ins(3,4,5,6)P4 plus AMPPNP
ComponentsINOSITOL-PENTAKISPHOSPHATE 2-KINASE
KeywordsTRANSFERASE / INOSITOL KINASE / PHYTIC ACID / PROTEIN KINASE / INOSITIDE SIGNALLING
Function / homology
Function and homology information


inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium ...inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Inositol-pentakisphosphate 2-kinase, N-lobe / Inositol-pentakisphosphate 2-kinase / Inositol-pentakisphosphate 2-kinase, N-terminal lobe / Inositol-pentakisphosphate 2-kinase / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Myo inositol 3,4,5,6 tetrakisphosphate / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsI Banos-Sanz, J. / Sanz-Aparicio, J. / Gonzalez, B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Conformational Changes Undergone by Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase Upon Substrate Binding: The Role of N-Lobe and Enantiomeric Substrate Preference
Authors: Banos-Sanz, J.I. / Sanz-Aparicio, J. / Whitfield, H. / Hamilton, C. / Brearley, C.A. / Gonzalez, B.
History
DepositionJun 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Jul 24, 2013Group: Refinement description
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_id / _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-PENTAKISPHOSPHATE 2-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3934
Polymers51,3211
Non-polymers1,0723
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.620, 65.080, 122.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INOSITOL-PENTAKISPHOSPHATE 2-KINASE / INOSITOL 1\ / 3\ / 4\ / 5\ / 6-PENTAKISPHOSPHATE 2-KINASE / INOSITOL-1\ / 3\ / 4\ / 5\ / 6- ...INOSITOL 1\ / 3\ / 4\ / 5\ / 6-PENTAKISPHOSPHATE 2-KINASE / INOSITOL-1\ / 3\ / 4\ / 5\ / 6-PENTAKISPHOSPHATE 2-KINASE / INS(1\ / 3\ / 4\ / 5\ / 6)P5 2-KINASE / ATIPK1 / INSP5 2-KINASE


Mass: 51321.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q93YN9, inositol-pentakisphosphate 2-kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-4MY / Myo inositol 3,4,5,6 tetrakisphosphate


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4

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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: 2.42 Å3/Da / Density % sol: 49.21 % / Description: NONE
Crystal growpH: 5.9 / Details: 21% PEG 3350, BIS-TRIS PH 5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.93→57.47 Å / Num. obs: 11132 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.4
Reflection shellResolution: 2.93→3.09 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XAN

2xan


Resolution: 2.93→57.42 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.819 / SU B: 36.764 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27916 531 4.8 %RANDOM
Rwork0.22465 ---
obs0.22717 10560 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.187 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--2.82 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.93→57.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 60 0 3320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023388
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0622.0014580
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7455407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9724.437151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88915622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0781520
X-RAY DIFFRACTIONr_chiral_restr0.0660.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212475
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.93→3.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 26 -
Rwork0.288 681 -
obs--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)
11.30870.0484-0.29591.27740.44692.46840.06590.2042-0.1066-0.1231-0.03690.03280.2786-0.1147-0.0290.09290.0122-0.0030.1275-0.01630.1147-14.1761-18.3896-17.0195
21.21230.43861.17622.2567-0.62312.194-0.13980.06290.1474-0.08540.039-0.1277-0.5227-0.25640.10080.32480.19990.08640.26090.05450.2315-18.54722.6177-19.4851
31.0020.3463-0.91962.06970.42284.23670.06290.02910.00240.1752-0.05220.09260.0522-0.0901-0.01070.03480.0263-0.01560.13170.04780.1308-10.6687-11.6244-5.0948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A118 - 323
2X-RAY DIFFRACTION2A3 - 117
3X-RAY DIFFRACTION3A324 - 437

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