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- PDB-7tn5: Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1... -

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Basic information

Entry
Database: PDB / ID: 7tn5
TitleCrystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 (ITPK1)
ComponentsInositol-tetrakisphosphate 1-kinase 1
KeywordsTRANSFERASE / ATP-grasp / inositol phosphate / InsP6 / 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: 2.9 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)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)37,3922
Polymers37,3561
Non-polymers351
Water1,820101
1
A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules

A: Inositol-tetrakisphosphate 1-kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7844
Polymers74,7132
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area2560 Å2
ΔGint-37 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.883, 98.883, 215.915
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: 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-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.: 101 / 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: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M potassium sodium tartrate, 100 mM imidazole, pH 8.0, 200 mM sodium chloride
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2019
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: 14458 / % possible obs: 98.4 % / Redundancy: 13 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.019 / Rrim(I) all: 0.071 / Χ2: 0.944 / Net I/σ(I): 12.7 / Num. measured all: 188525
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.95130.8737000.9310.2450.9070.88799.6
2.95-313.30.6877180.9580.1910.7130.91399
3-3.0613.30.596910.9610.1640.6130.9199.3
3.06-3.1213.20.5557130.9740.1550.5770.89299.4
3.12-3.1913.40.4027040.9830.1120.4170.91698.9
3.19-3.2713.30.3227090.9850.090.3340.93699.4
3.27-3.3513.20.2697050.9910.0750.2790.96998.9
3.35-3.4413.20.1937160.9940.0540.2011.05898.9
3.44-3.5413.20.1547260.9950.0430.161.00999.2
3.54-3.6513.30.1177000.9970.0330.1221.04899
3.65-3.7813.20.0967170.9970.0270.11.04498.9
3.78-3.9413.30.0837080.9980.0230.0860.95498.5
3.94-4.1113.10.0657220.9970.0180.0670.9898.8
4.11-4.3313.20.0527200.9980.0150.0540.99798.4
4.33-4.613.10.0437260.9990.0120.0441.05998.5
4.6-4.96130.0417370.9980.0110.0421.21298.3
4.96-5.4613.10.0377230.9990.010.0380.95897.8
5.46-6.2412.80.0347490.9990.010.0350.80397.4
6.24-7.8612.70.0267470.9990.0080.0280.6796.5
7.86-5011.40.0228270.9980.0070.0230.65594.7

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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: 2.9→49.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.903 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.356 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 730 5.1 %RANDOM
Rwork0.1771 ---
obs0.1797 13628 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.5 Å2 / Biso mean: 48.537 Å2 / Biso min: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 2.9→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 1 101 2209
Biso mean--30.25 42.57 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132165
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172063
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.6352945
X-RAY DIFFRACTIONr_angle_other_deg1.2581.5724759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5695266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03420.811111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47815339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5941516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 47 -
Rwork0.206 968 -
all-1015 -
obs--98.83 %

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