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- PDB-7vce: Structural studies of human inositol monophosphatase-1 inhibition... -

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Basic information

Entry
Database: PDB / ID: 7vce
TitleStructural studies of human inositol monophosphatase-1 inhibition by ebselen
ComponentsInositol monophosphatase 1
KeywordsHYDROLASE / IMPase1 / Ebselen
Function / homology
Function and homology information


D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / lithium ion binding / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process ...D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / lithium ion binding / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphatidylinositol biosynthetic process / phosphate-containing compound metabolic process / phosphatidylinositol phosphate biosynthetic process / manganese ion binding / magnesium ion binding / signal transduction / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Inositol monophosphatase, lithium-sensitive / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family
Similarity search - Domain/homology
Inositol monophosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAbuhammad, A. / Laurieri, N. / Rice, A. / Lowe, E.D. / McDonough, M.A. / Singh, N. / Churchill, G.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2023
Title: Structural and biochemical analysis of human inositol monophosphatase-1 inhibition by ebselen.
Authors: Abuhammad, A. / Laurieri, N. / Rice, A. / Lowe, E.D. / Singh, N. / Naser, S.M. / Ratrout, S.S. / Churchill, G.C.
History
DepositionSep 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol monophosphatase 1
B: Inositol monophosphatase 1


Theoretical massNumber of molelcules
Total (without water)59,8052
Polymers59,8052
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-20 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.290, 75.720, 57.510
Angle α, β, γ (deg.)90.000, 95.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Inositol monophosphatase 1 / IMP 1 / IMPase 1 / D-galactose 1-phosphate phosphatase / Inositol-1(or 4)-monophosphatase 1 / ...IMP 1 / IMPase 1 / D-galactose 1-phosphate phosphatase / Inositol-1(or 4)-monophosphatase 1 / Lithium-sensitive myo-inositol monophosphatase A1


Mass: 29902.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IMPA1, IMPA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P29218, inositol-phosphate phosphatase, D-galactose 1-phosphate phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate and 20% (wt/vol) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→45.04 Å / Num. obs: 14825 / % possible obs: 98.75 % / Redundancy: 1.8 % / CC1/2: 0.993 / Net I/σ(I): 8.57
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 1390 / CC1/2: 0.733

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AS4

4as4


Resolution: 2.6→45.04 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: FREE R-VALUE / ESU R: 0.742 / ESU R Free: 0.309
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2436 764 5.164 %
Rwork0.2006 17850 -
all0.23 --
obs-14825 98.78 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 37.693 Å2
Baniso -1Baniso -2Baniso -3
1-1.162 Å2-0 Å2-2.299 Å2
2--0.626 Å20 Å2
3----1.312 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 0 128 3835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123835
X-RAY DIFFRACTIONr_bond_other_d0.0550.0173715
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.6275210
X-RAY DIFFRACTIONr_angle_other_deg1.8931.5688453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0125505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41122.883163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18115630
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.034159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8671518
X-RAY DIFFRACTIONr_chiral_restr0.060.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02841
X-RAY DIFFRACTIONr_nbd_refined0.1860.2798
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23642
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21904
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.22255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2940.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0730.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.28
X-RAY DIFFRACTIONr_nbd_other0.2420.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3790.22
X-RAY DIFFRACTIONr_mcbond_it1.6793.4332023
X-RAY DIFFRACTIONr_mcbond_other1.7143.4322022
X-RAY DIFFRACTIONr_mcangle_it2.7635.1382527
X-RAY DIFFRACTIONr_mcangle_other2.785.1412528
X-RAY DIFFRACTIONr_scbond_it1.7033.5791812
X-RAY DIFFRACTIONr_scbond_other1.7433.5761811
X-RAY DIFFRACTIONr_scangle_it2.6845.3262683
X-RAY DIFFRACTIONr_scangle_other2.6955.3292684
X-RAY DIFFRACTIONr_lrange_it4.22241.0874244
X-RAY DIFFRACTIONr_lrange_other4.16841.1034219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.7480.335820.2811261X-RAY DIFFRACTION98.1725
2.748-2.8510.319540.2861242X-RAY DIFFRACTION99.3103
2.851-2.9670.254610.2511210X-RAY DIFFRACTION99.2194
2.967-3.0990.315610.2291135X-RAY DIFFRACTION99.0887
3.099-3.250.264500.2441122X-RAY DIFFRACTION99.4063
3.25-3.4250.304540.2111041X-RAY DIFFRACTION99.7268
3.425-3.6320.289550.201996X-RAY DIFFRACTION99.3384
3.632-3.8820.214510.19914X-RAY DIFFRACTION99.7932
3.882-4.1910.238540.184878X-RAY DIFFRACTION99.7859
4.191-4.5880.178530.167791X-RAY DIFFRACTION99.6458
4.588-5.1260.198370.168741X-RAY DIFFRACTION99.2347
5.126-5.9110.289370.216643X-RAY DIFFRACTION99.7067
5.911-7.220.279250.207554X-RAY DIFFRACTION99.3139
7.22-10.1310.193300.163420X-RAY DIFFRACTION99.5575
10.131-45.040.27110.262254X-RAY DIFFRACTION98.1481

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