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- PDB-7tn3: Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1... -

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Basic information

Entry
Database: PDB / ID: 7tn3
TitleCrystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 mutant (ZmITPK1-F189A/H192A)
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 / myo-inositol hexakisphosphate biosynthetic process / inositol hexakisphosphate 5-kinase activity / 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 / myo-inositol hexakisphosphate biosynthetic process / inositol hexakisphosphate 5-kinase activity / seed development / inositol-1,3,4,5-tetrakisphosphate 6-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
Inositol-tetrakisphosphate 1-kinase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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)1ZI AES080046-31 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)37,2052
Polymers37,1691
Non-polymers351
Water61334
1
A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules

A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4094
Polymers74,3392
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area3070 Å2
ΔGint-40 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.594, 98.594, 202.571
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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: 37169.281 Da / Num. of mol.: 1 / Mutation: F189A/H192A
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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.8 Å3/Da / Density % sol: 67.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG3350, 100 mM HEPES, pH 7.0, 200 mM calicum acetate, 10% glycerol
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: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 13583 / % possible obs: 99.9 % / Redundancy: 23.8 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.021 / Rrim(I) all: 0.099 / Χ2: 1.022 / Net I/σ(I): 10.7 / Num. measured all: 323556
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.9525.60.9656360.9630.1930.9850.88100
2.95-325.10.8956760.9450.1810.9130.905100
3-3.0624.50.8046510.9480.1650.8210.899100
3.06-3.1223.80.7036530.970.1460.7180.905100
3.12-3.1921.50.5186610.9760.1140.530.928100
3.19-3.2724.40.4366680.980.0890.4450.959100
3.27-3.3526.50.3376590.9940.0660.3430.954100
3.35-3.4426.30.2726690.9930.0540.2780.978100
3.44-3.5426.30.2216630.9970.0440.2261.041100
3.54-3.65260.1856700.9970.0370.1891.17100
3.65-3.7825.40.1446750.9950.0290.1471.063100
3.78-3.9425.20.1316690.9970.0270.1341.09699.9
3.94-4.1124.30.1076670.9970.0230.1091.11299.6
4.11-4.3323.20.0896770.9980.0190.0911.08999.7
4.33-4.620.70.0756770.9970.0180.0771.03199.7
4.6-4.9619.80.0646860.9980.0160.0660.97599.4
4.96-5.4623.40.0656910.9990.0150.0671.01299.7
5.46-6.2423.70.0657050.9980.0140.0660.96399.9
6.24-7.8622.30.0627230.9980.0140.0631.029100
7.86-5019.60.078070.9870.0170.0721.43499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.35 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.851 / SU B: 12.547 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.522 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2803 654 5.1 %RANDOM
Rwork0.229 ---
obs0.2316 12186 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.94 Å2 / Biso mean: 50.937 Å2 / Biso min: 12.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å2-0 Å2
2---0.13 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2.9→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 1 34 2116
Biso mean--27.65 39.93 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132144
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172054
X-RAY DIFFRACTIONr_angle_refined_deg1.9661.6342917
X-RAY DIFFRACTIONr_angle_other_deg1.2321.5714734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1875267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45520.833108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.6415336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9551516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02465
LS refinement shellResolution: 2.902→2.977 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 25 -
Rwork0.285 522 -
all-547 -
obs--56.68 %

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