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- PDB-7tn6: Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1... -

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Basic information

Entry
Database: PDB / ID: 7tn6
TitleCrystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 mutant (ZmITPK1-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 / 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
Similarity search - Domain/homology
Inositol-tetrakisphosphate 1-kinase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 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)37,3252
Polymers37,2891
Non-polymers351
Water28816
1
A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules

A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6504
Polymers74,5792
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area3220 Å2
ΔGint-36 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.161, 98.161, 202.430
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-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.: 16 / 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: 3.77 Å3/Da / Density % sol: 67.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG3350, 100mM HEPES 7.0, 200mM CaAc2 and 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: 2.85→50 Å / Num. obs: 14039 / % possible obs: 98.6 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 0.975 / Net I/σ(I): 12 / Num. measured all: 180691
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.913.30.8166780.9150.2280.8480.9698.8
2.9-2.9513.30.6276870.9520.1750.6520.96399.4
2.95-3.01130.5546740.9320.1570.5770.9599.4
3.01-3.0712.70.5196990.9460.1490.5410.98898.6
3.07-3.1412.10.4026810.9490.1190.420.99299.4
3.14-3.2112.10.3126360.9690.0910.3260.93192.7
3.21-3.2913.70.36980.9850.0830.3121.00299.1
3.29-3.3813.70.2266790.990.0620.2351.00699.1
3.38-3.4813.80.1766930.9940.0490.1831.00199.6
3.48-3.5913.70.1466910.9960.040.1521.00399.1
3.59-3.7213.40.1146950.9960.0320.1191.05199.3
3.72-3.8713.10.17040.9950.0290.1040.96299.4
3.87-4.0413.20.0867000.9970.0250.090.96599.4
4.04-4.2612.80.0747130.9960.0210.0770.95499.2
4.26-4.5212.10.0616970.9950.0180.0640.86999.1
4.52-4.87120.0576770.9950.0180.060.82594.6
4.87-5.3613.50.0617260.9790.0180.0640.89399.2
5.36-6.1413.20.0577430.9940.0170.060.8799.6
6.14-7.7312.50.0567390.9970.0170.0590.85899.2
7.73-5010.70.0628290.9910.020.0651.44397.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→47.74 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.87 / SU B: 11.258 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.438 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.271 700 5.1 %RANDOM
Rwork0.2244 ---
obs0.2269 13136 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.01 Å2 / Biso mean: 53.865 Å2 / Biso min: 13.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å2-0 Å2
2---0.03 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.85→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 1 16 2086
Biso mean--28.44 35.45 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132143
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172047
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.6352915
X-RAY DIFFRACTIONr_angle_other_deg1.2661.5714718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1995266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84820.826109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97215335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3391516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
LS refinement shellResolution: 2.85→2.922 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.339 41 -
Rwork0.259 819 -
obs--84.81 %

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