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- PDB-7tn8: Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1... -

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Basic information

Entry
Database: PDB / ID: 7tn8
TitleCrystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 mutant (ZmITPK1-H192A) in complex with InsP6
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 / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity ...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 / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / seed development / 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 / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Inositol-tetrakisphosphate 1-kinase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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)37,9853
Polymers37,2891
Non-polymers6952
Water1,71195
1
A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules

A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9706
Polymers74,5792
Non-polymers1,3914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area3950 Å2
ΔGint-53 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.070, 99.070, 215.444
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: 37289.387 Da / Num. of mol.: 1 / Mutation: 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-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 / 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.: 95 / 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: 4.09 Å3/Da / Density % sol: 69.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG3350, 100 mM HEPES, 7.0, 200 mM calcium chloride, 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 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20094 / % possible obs: 99.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.023 / Rrim(I) all: 0.07 / Χ2: 0.97 / Net I/σ(I): 15.5 / Num. measured all: 199201
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6410.60.8499740.8810.2690.8911.02499.8
2.64-2.6910.50.7779680.8650.2480.8171.02799.9
2.69-2.7410.30.5899780.9140.190.6191.036100
2.74-2.810.20.4799730.9340.1550.5041.041100
2.8-2.8610.20.3919940.9520.1270.4121.023100
2.86-2.93100.3139840.970.1030.331.018100
2.93-39.20.2269890.9850.0780.241.013100
3-3.0890.189800.9870.0630.1910.982100
3.08-3.1710.60.1579900.9930.050.1650.951100
3.17-3.2810.70.1179890.9960.0370.1230.908100
3.28-3.3910.60.0979850.9960.0310.1020.894100
3.39-3.5310.40.07110120.9970.0230.0750.861100
3.53-3.6910.30.0599970.9970.0190.0620.79100
3.69-3.8810.10.0519910.9990.0170.0540.7699.9
3.88-4.139.80.04410230.9990.0150.0460.73599.8
4.13-4.458.70.04110120.9980.0150.0440.74799.8
4.45-4.899.50.03810120.9980.0130.040.69799.1
4.89-5.69.90.04110270.9980.0140.0430.77398.4
5.6-7.059.70.04810670.9970.0160.051.0899.9
7.05-508.40.06711490.9820.0250.0722.08997.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→42.11 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.757 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2517 996 5 %RANDOM
Rwork0.2021 ---
obs0.2047 18995 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.82 Å2 / Biso mean: 43.691 Å2 / Biso min: 10.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å2-0 Å2
2---0.24 Å20 Å2
3---0.77 Å2
Refinement stepCycle: final / Resolution: 2.6→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 37 95 2316
Biso mean--80.85 41.08 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132278
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172132
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.6583109
X-RAY DIFFRACTIONr_angle_other_deg1.2781.5794927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9565278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21421.14114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7715349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6431516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022508
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02484
LS refinement shellResolution: 2.6→2.663 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.359 72 -
Rwork0.264 1295 -
obs--94.67 %

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