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- PDB-2bji: High Resolution Structure of myo-Inositol Monophosphatase, The Ta... -

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Basic information

Entry
Database: PDB / ID: 2bji
TitleHigh Resolution Structure of myo-Inositol Monophosphatase, The Target of Lithium Therapy
ComponentsINOSITOL-1(OR 4)-MONOPHOSPHATASE
KeywordsHYDROLASE / ASPARTIC PROTEINASE MECHANISM / ASPARTYL PROTEASE / SUCCINIMIDE / ZYMOGEN
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 / inositol metabolic process ...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 phosphate biosynthetic process / manganese ion binding / magnesium ion binding / signal transduction / 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
Inositol monophosphatase 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsGill, R. / Mohammed, F. / Badyal, R. / Coates, L. / Erskine, P. / Thompson, D. / Cooper, J. / Gore, M. / Wood, S.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005
Title: High-resolution structure of myo-inositol monophosphatase, the putative target of lithium therapy.
Authors: Gill, R. / Mohammed, F. / Badyal, R. / Coates, L. / Erskine, P. / Thompson, D. / Cooper, J. / Gore, M. / Wood, S.
History
DepositionFeb 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Advisory / Database references / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSITOL-1(OR 4)-MONOPHOSPHATASE
B: INOSITOL-1(OR 4)-MONOPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3198
Polymers60,1732
Non-polymers1466
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.230, 55.150, 60.880
Angle α, β, γ (deg.)67.22, 69.65, 85.14
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 30086.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Organ: BRAIN / Plasmid: PRSET5A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20456, inositol-phosphate phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: ROOM TEMP, VAPOUR DIFFUSION. HANGING DROPS FROM MIXING EQUAL VOLUMES (2 MICRO LITRES) PROTEIN (CONCENTRATION 20 MG/ML BOVINE IMPASE IN 20 MM TRIS.HCL PH 7.5 CONTAINING 20 MM MGCL2) WITH ...Details: ROOM TEMP, VAPOUR DIFFUSION. HANGING DROPS FROM MIXING EQUAL VOLUMES (2 MICRO LITRES) PROTEIN (CONCENTRATION 20 MG/ML BOVINE IMPASE IN 20 MM TRIS.HCL PH 7.5 CONTAINING 20 MM MGCL2) WITH RESERVOIR SOLUTION (0.1 M SODIUM ACETATE, 0.1 M SODIUM HEPES PH 8.5 AND 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→27.1 Å / Num. obs: 89508 / % possible obs: 84.7 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.7 / % possible all: 41.8

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HHM

2hhm


Resolution: 1.24→10 Å / Num. parameters: 41267 / Num. restraintsaints: 50584 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: INITIAL REFINEMENT DONE WITH CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4685 5 %RANDOM
obs0.153 -84.7 %-
all-93951 --
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 4127 / Occupancy sum non hydrogen: 4510
Refinement stepCycle: LAST / Resolution: 1.24→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 6 518 4688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0272
X-RAY DIFFRACTIONs_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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