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- PDB-6zk0: 1.47A human IMPase with ebselen -

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Basic information

Entry
Database: PDB / ID: 6zk0
Title1.47A human IMPase with ebselen
ComponentsInositol monophosphatase 1
KeywordsHYDROLASE / Inhibitor / Complex / phosphatase
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 / cytoplasm / cytosol
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
N-phenyl-2-selanylbenzamide / : / Inositol monophosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.47 Å
AuthorsBax, B.D. / Fenn, G.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystallization and structure of ebselen bound to Cys141 of human inositol monophosphatase.
Authors: Fenn, G.D. / Waller-Evans, H. / Atack, J.R. / Bax, B.D.
History
DepositionJun 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 12, 2023Group: Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Inositol monophosphatase 1
BBB: Inositol monophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,03030
Polymers60,7482
Non-polymers2,28228
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-180 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.020, 84.020, 150.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AAABBB

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


Mass: 30373.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IMPA1, IMPA / Cell line (production host): BL21 Rosetta 2(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P29218, inositol-phosphate phosphatase, D-galactose 1-phosphate phosphatase

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Non-polymers , 7 types, 454 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2M MnS04, 0.1M MES, 28% PEG4000 and pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 1.47→24.44 Å / Num. obs: 104886 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Net I/σ(I): 20.4
Reflection shellResolution: 1.47→1.5 Å / Rmerge(I) obs: 2.019 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5118 / CC1/2: 0.498 / Rpim(I) all: 0.652 / Rrim(I) all: 2.123

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6gj0

6gj0


Resolution: 1.47→24.438 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.565 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2083 5081 4.847 %
Rwork0.1791 99740 -
all0.181 --
obs-104821 99.966 %
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: 30.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.032 Å2-0.016 Å20 Å2
2---0.032 Å20 Å2
3---0.103 Å2
Refinement stepCycle: LAST / Resolution: 1.47→24.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 122 426 4654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124813
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.6326563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4115.016644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.522.353221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78315808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4691531
X-RAY DIFFRACTIONr_chiral_restr0.140.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023723
X-RAY DIFFRACTIONr_nbd_refined0.2410.22642
X-RAY DIFFRACTIONr_nbtor_refined0.3230.23237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2760.2546
X-RAY DIFFRACTIONr_metal_ion_refined0.3590.229
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1090.21
X-RAY DIFFRACTIONr_mcbond_it2.5672.7052451
X-RAY DIFFRACTIONr_mcangle_it3.5364.0413130
X-RAY DIFFRACTIONr_scbond_it3.843.1292361
X-RAY DIFFRACTIONr_scangle_it5.2764.5483430
X-RAY DIFFRACTIONr_lrange_it6.85439.548021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.47-1.5080.3623360.30672930.30876320.7080.76499.96070.298
1.508-1.5490.3253550.30471000.30574550.7880.7731000.289
1.549-1.5940.3113530.27268840.27472370.8310.8521000.249
1.594-1.6430.2643260.24567290.24670550.8970.8971000.217
1.643-1.6960.2623590.22664860.22868450.9080.9131000.196
1.696-1.7560.2542990.22163290.22266280.9090.9241000.188
1.756-1.8220.2363030.20360950.20463980.9240.9361000.174
1.822-1.8950.2372870.19258780.19461650.9250.9411000.167
1.895-1.9790.2253060.19256030.19459090.9370.9451000.168
1.979-2.0750.2292650.18854090.1956740.9380.951000.17
2.075-2.1870.2142410.1851630.18154040.9460.9531000.167
2.187-2.3180.2112900.17548340.17751240.9460.9551000.162
2.318-2.4760.2082470.17345830.17548300.9480.9551000.163
2.476-2.6730.2272080.17642930.17845010.9410.9471000.168
2.673-2.9240.1831900.16639980.16741880.9580.961000.164
2.924-3.2640.2211940.1735900.17237840.9440.9541000.174
3.264-3.7570.1791910.15231970.15333880.9640.9691000.161
3.757-4.5750.1571540.13927260.1428810.9740.97699.96530.156
4.575-6.3590.196950.1722110.17123060.9630.9691000.194
6.359-24.4380.195820.19913390.19914210.9740.9751000.227

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