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- PDB-7tn7: Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1... -

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Basic information

Entry
Database: PDB / ID: 7tn7
TitleCrystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 mutant (ZmITPK1 residues 18-218-Gly-Ser-Gly-Ser-Gly-248-328)
ComponentsInositol-tetrakisphosphate 1-kinase 1
KeywordsTRANSFERASE / ATP-grasp / inositol phosphate / kinase / signal transduction
Function / homology
Function and homology information


inositol-hexakisphosphate 5-kinase / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / myo-inositol hexakisphosphate biosynthetic process / seed development ...inositol-hexakisphosphate 5-kinase / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / myo-inositol hexakisphosphate biosynthetic process / seed development / inositol hexakisphosphate 5-kinase activity / inositol trisphosphate metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
Inositol-tetrakisphosphate 1-kinase, N-terminal / Inositol 1,3,4-trisphosphate 5/6-kinase pre-ATP-grasp domain / Inositol-tetrakisphosphate 1-kinase / Inositol 1,3,4-trisphosphate 5/6-kinase, ATP-grasp domain / Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain
Similarity search - Domain/homology
PHOSPHATE ION / Inositol-tetrakisphosphate 1-kinase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsZong, G. / Wang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046-31 United States
CitationJournal: Faseb J. / Year: 2022
Title: Structural and catalytic analyses of the InsP 6 kinase activities of higher plant ITPKs.
Authors: Zong, G. / Shears, S.B. / Wang, H.
History
DepositionJan 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4873
Polymers37,3561
Non-polymers1302
Water4,071226
1
A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules

A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9746
Polymers74,7132
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area2990 Å2
ΔGint-48 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.256, 99.256, 217.952
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-682-

HOH

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Components

#1: Protein Inositol-tetrakisphosphate 1-kinase 1 / Inositol 1 / 3 / 4-trisphosphate 5/6-kinase 1 / Inositol-triphosphate 5/6-kinase 1 / Ins(1 / 4)P(3) ...Inositol 1 / 3 / 4-trisphosphate 5/6-kinase 1 / Inositol-triphosphate 5/6-kinase 1 / Ins(1 / 4)P(3) 5/6-kinase 1 / Low phytic acid protein 2 / ZmIpk


Mass: 37356.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ITPK1, LPA2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q84Y01, inositol-tetrakisphosphate 1-kinase, inositol-1,3,4-trisphosphate 5/6-kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.15 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M ammonium phosphate dibasic, 20% ethylene glycol, 100 mM Tris, pH 8.0
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 30855 / % possible obs: 99.8 % / Redundancy: 34.7 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.01 / Rrim(I) all: 0.062 / Χ2: 1.105 / Net I/σ(I): 11.5 / Num. measured all: 1069688
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.2935.50.7515000.9630.1260.760.935100
2.29-2.3335.10.63214920.9660.1070.6410.944100
2.33-2.3834.80.53615210.9760.0910.5440.949100
2.38-2.4234.40.4414950.9850.0750.4460.961100
2.42-2.4833.50.3715360.9870.0640.3750.961100
2.48-2.5331.20.29515010.9920.0530.30.986100
2.53-2.629.30.27115210.9920.0510.2761.001100
2.6-2.6736.10.23315150.9960.0390.2370.992100
2.67-2.7537.50.18615230.9980.030.1881.017100
2.75-2.8337.70.14915240.9980.0240.1511.044100
2.83-2.9437.50.12315100.9990.020.1251.073100
2.94-3.0537.50.08915360.9990.0150.091.138100
3.05-3.1937.10.07715530.9990.0130.0781.194100
3.19-3.3636.80.062152910.010.0631.28100
3.36-3.5736.20.051156010.0080.0521.432100
3.57-3.8535.50.044155010.0070.0451.46799.9
3.85-4.2333.90.039156510.0070.0391.34799.5
4.23-4.8528.70.034155310.0060.0341.29197.9
4.85-6.1330.03216100.9990.0060.0331.05499
6.1-5032.50.03717610.9970.0070.0380.99999

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data collection
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.25→46.06 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.16 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1515 4.9 %RANDOM
Rwork0.1932 ---
obs0.1946 29271 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.1 Å2 / Biso mean: 36.736 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å2-0 Å2
2---0.08 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 2.25→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 6 226 2321
Biso mean--58.8 42.48 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132183
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172079
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.6352969
X-RAY DIFFRACTIONr_angle_other_deg1.3851.5724796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5695268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17520.982112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19515343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5891516
X-RAY DIFFRACTIONr_chiral_restr0.0980.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
LS refinement shellResolution: 2.253→2.311 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 107 -
Rwork0.253 2106 -
all-2213 -
obs--99.64 %

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