[English] 日本語
Yorodumi
- PDB-7tn3: Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more