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- PDB-4as5: Structure of mouse inositol monophosphatase 1 -

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Basic information

Entry
Database: PDB / ID: 4as5
TitleStructure of mouse inositol monophosphatase 1
ComponentsINOSITOL MONOPHOSPHATASE 1
KeywordsHYDROLASE / LITHIUM / BIPOLAR DISORDER
Function / homology
Function and homology information


Synthesis of IP2, IP, and Ins in the cytosol / D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / : / lithium ion binding / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity ...Synthesis of IP2, IP, and Ins in the cytosol / D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / : / 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 / axon / neuronal cell body / magnesium ion binding / signal transduction / protein homodimerization activity / identical protein binding / 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 / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...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 / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / PHOSPHATE ION / Inositol monophosphatase 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSingh, N. / Knight, M. / Halliday, A.C. / Lack, N.A. / Lowe, E.D. / Churchill, G.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Cloning, Expression, Purification, Crystallization and X-Ray Analysis of Inositol Monophosphatase from Mus Musculus and Homo Sapiens.
Authors: Singh, N. / Halliday, A.C. / Knight, M. / Lack, N.A. / Lowe, E.D. / Churchill, G.C.
History
DepositionApr 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSITOL MONOPHOSPHATASE 1
B: INOSITOL MONOPHOSPHATASE 1
C: INOSITOL MONOPHOSPHATASE 1
D: INOSITOL MONOPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,15336
Polymers121,8454
Non-polymers2,30832
Water15,277848
1
A: INOSITOL MONOPHOSPHATASE 1
B: INOSITOL MONOPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,13619
Polymers60,9222
Non-polymers1,21417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-21.3 kcal/mol
Surface area25240 Å2
MethodPISA
2
C: INOSITOL MONOPHOSPHATASE 1
D: INOSITOL MONOPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,01717
Polymers60,9222
Non-polymers1,09415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-22.5 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.785, 81.490, 97.139
Angle α, β, γ (deg.)90.00, 113.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.663, 0.114, 0.74), (0.116, -0.992, 0.049), (0.74, 0.054, -0.671)-46.413, 42.099, 98.113
2given(-0.892, 0.382, -0.242), (0.366, 0.295, -0.882), (-0.266, -0.876, -0.403)41.25, 72.277, 121.579
3given(-0.742, -0.385, -0.548), (-0.464, -0.295, 0.835), (-0.483, 0.875, 0.04)78.854, -18.892, 51.332

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
INOSITOL MONOPHOSPHATASE 1 / / IMP 1 / IMPASE 1 / INOSITOL-1(OR 4)- MONOPHOSPHATASE 1 / LITHIUM-SENSITIVE MYO-INOSITOL MONOPHOSPHATASE A1


Mass: 30461.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PRSET5A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR(DE3) / Variant (production host): PLYSS / References: UniProt: O55023, inositol-phosphate phosphatase

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Non-polymers , 6 types, 880 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.96 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M NAI, 20% W/V PEG 3350, 0.1 M BIS TRIS PROPANE AT PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2011 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SINGLE BOUNCE SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.43→43.34 Å / Num. obs: 46562 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.4
Reflection shellResolution: 2.43→2.56 Å / Redundancy: 6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 96.7

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HHM

2hhm


Resolution: 2.43→43.34 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9213 / SU R Cruickshank DPI: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.47 / SU Rfree Blow DPI: 0.237 / SU Rfree Cruickshank DPI: 0.233
Details: NOTE 1 :IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9288. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: NOTE 1 :IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9288. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=12.
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 2316 5 %RANDOM
Rwork0.1602 ---
obs0.1629 46280 98.67 %-
Displacement parametersBiso mean: 41.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.7354 Å20 Å2-3.4056 Å2
2---4.2865 Å20 Å2
3---5.0219 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: LAST / Resolution: 2.43→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8368 0 73 848 9289
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018555HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2411546HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3035SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes208HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1226HARMONIC5
X-RAY DIFFRACTIONt_it8555HARMONIC20
X-RAY DIFFRACTIONt_nbd12SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion17.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1169SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10478SEMIHARMONIC4
LS refinement shellResolution: 2.43→2.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 172 5.11 %
Rwork0.1917 3191 -
all0.1969 3363 -
obs--98.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5417-0.2768-0.42381.7091-0.62531.4548-0.0054-0.1639-0.2007-0.00230.08670.26320.11560.0648-0.0812-0.13690.00180.002-0.12910.05070.043330.795617.767587.6863
20.81940.1373-0.2020.7811-0.3652.04280.01680.11880.1288-0.11540.019-0.03490.02270.1701-0.0358-0.1269-0.01690.0227-0.08280.0330.04740.598932.476862.9583
31.2299-0.4492-0.41613.17010.8841.66040.0543-0.022-0.11090.3799-0.15720.20430.3296-0.1150.1029-0.2202-0.05530.0538-0.1165-0.17190.0516-1.73349.627564.3734
41.8277-0.0406-0.26312.47240.67141.33010.14610.14560.4041-0.2004-0.22960.1386-0.2391-0.18940.0835-0.24680.06820.0511-0.1059-0.06270.0851.082139.459858.3194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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