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- PDB-1imb: STRUCTURAL ANALYSIS OF INOSITOL MONOPHOSPHATASE COMPLEXES WITH SU... -

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Basic information

Entry
Database: PDB / ID: 1imb
TitleSTRUCTURAL ANALYSIS OF INOSITOL MONOPHOSPHATASE COMPLEXES WITH SUBSTRATES
ComponentsINOSITOL MONOPHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / glucose-1-phosphatase activity / glycerol-2-phosphatase activity / glucose-6-phosphatase activity / inositol monophosphate 4-phosphatase activity / fructose-1-phosphatase activity / inositol monophosphate 3-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / lithium ion binding ...D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / glucose-1-phosphatase activity / glycerol-2-phosphatase activity / glucose-6-phosphatase activity / inositol monophosphate 4-phosphatase activity / fructose-1-phosphatase activity / inositol monophosphate 3-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / lithium ion binding / inositol biosynthetic process / inositol-phosphate phosphatase / 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 / 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
GADOLINIUM ATOM / L-MYO-INOSITOL-1-PHOSPHATE / Inositol monophosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsBone, R.
Citation
Journal: Biochemistry / Year: 1994
Title: Structural analysis of inositol monophosphatase complexes with substrates.
Authors: Bone, R. / Frank, L. / Springer, J.P. / Pollack, S.J. / Osborne, S.A. / Atack, J.R. / Knowles, M.R. / McAllister, G. / Ragan, C.I. / Broughton, H.B. / Baker, R. / Fletcher, S.R.
#1: Journal: Biochem.J. / Year: 1992
Title: Cdna Cloning of Human and Rat Brain Myo-Inositol Monophosphatase. Expression and Characterization of the Human Recombinant Enzyme
Authors: Mcallister, G. / Whiting, P. / Hammond, E.A. / Knowles, M.R. / Atack, J.R. / Bailey, F.J. / Maigetter, R. / Ragan, C.I.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Structure of Inositol Monophosphatase, the Putative Target of Lithium Therapy
Authors: Bone, R. / Springer, J.P. / Atack, J.R.
History
DepositionFeb 8, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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
B: INOSITOL MONOPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2706
Polymers60,4402
Non-polymers8314
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-40 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.900, 86.900, 154.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO A 186 / 2: CIS PROLINE - PRO B 186

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Components

#1: Protein INOSITOL MONOPHOSPHATASE


Mass: 30219.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA / Organ: BRAIN / References: UniProt: P29218, inositol-phosphate phosphatase
#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-LIP / L-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop / Details: Bone, R., (1992) Proc.Nat.Acad.Sci.USA, 89, 10031.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
164-68 %sat1reservoirLi2SO4
25 mMglutathione1reservoir
33 mM1reservoirNaN3
42-6 mM1reservoirGd2(SO4)3can be replaced with 5mM CaSO4
510 mg/mlinositol monophosphatase1drop
620 mMTris-HCl1drop
71 mMEGTA1drop
82 mMo-phenanthroline1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / % possible obs: 84 % / Observed criterion σ(I): 19.1 / Rmerge(I) obs: 0.075

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→8 Å / Rfactor Rwork: 0.167 / Rfactor obs: 0.167 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 34 200 4380
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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