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- PDB-6gj0: Human IMPase with Mn -

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Basic information

Entry
Database: PDB / ID: 6gj0
TitleHuman IMPase with Mn
ComponentsInositol monophosphatase 1
KeywordsHYDROLASE / IMPase / Complex / Lithium
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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKraft, L.V. / Roe, S.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Co-crystallization of human inositol monophosphatase with the lithium mimetic L-690,330.
Authors: Kraft, L. / Roe, S.M. / Gill, R. / Atack, J.R.
History
DepositionMay 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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_asym_id / _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_asym_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,71216
Polymers60,4402
Non-polymers1,27314
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-45 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.940, 84.940, 152.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

21A-679-

HOH

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Components

#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: 30219.781 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 (E. coli)
References: UniProt: P29218, inositol-phosphate phosphatase, D-galactose 1-phosphate phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Equal volumes (1 uL) of the protein in storage buffer (20 mg/mL) and reservoir solution (0.12 M MnSO4, 0.1 M MES pH 5.5, 24 % (w/v) PEG 4000) were mixed.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.73→42.47 Å / Num. obs: 67109 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 21.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.03 / Rrim(I) all: 0.069 / Net I/σ(I): 16.9
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4858 / CC1/2: 0.737 / Rpim(I) all: 0.353 / Rrim(I) all: 0.809 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AS4

4as4


Resolution: 1.73→42.47 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.21 6124 4.85 %
Rwork0.1712 --
obs0.173 67051 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4138 0 66 509 4713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074356
X-RAY DIFFRACTIONf_angle_d1.1215901
X-RAY DIFFRACTIONf_dihedral_angle_d14.4141612
X-RAY DIFFRACTIONf_chiral_restr0.043681
X-RAY DIFFRACTIONf_plane_restr0.005756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.74970.33021940.30053998X-RAY DIFFRACTION99
1.7497-1.77030.28872150.28474040X-RAY DIFFRACTION98
1.7703-1.79190.2952050.27493932X-RAY DIFFRACTION98
1.7919-1.81450.28912260.26193943X-RAY DIFFRACTION98
1.8145-1.83840.28352120.23914064X-RAY DIFFRACTION99
1.8384-1.86360.25521660.22874010X-RAY DIFFRACTION99
1.8636-1.89020.26991870.22554128X-RAY DIFFRACTION99
1.8902-1.91840.25342060.2174020X-RAY DIFFRACTION99
1.9184-1.94840.24371400.22154001X-RAY DIFFRACTION99
1.9484-1.98040.28742190.20564102X-RAY DIFFRACTION99
1.9804-2.01450.17532220.19263936X-RAY DIFFRACTION99
2.0145-2.05110.25682220.19153996X-RAY DIFFRACTION99
2.0511-2.09060.22172320.19223988X-RAY DIFFRACTION99
2.0906-2.13330.2652160.19054024X-RAY DIFFRACTION98
2.1333-2.17960.24062210.18473992X-RAY DIFFRACTION98
2.1796-2.23030.21162380.18223982X-RAY DIFFRACTION99
2.2303-2.28610.2231440.1714075X-RAY DIFFRACTION99
2.2861-2.34790.21912060.16734019X-RAY DIFFRACTION99
2.3479-2.4170.2172840.17243958X-RAY DIFFRACTION98
2.417-2.4950.21292050.17044057X-RAY DIFFRACTION99
2.495-2.58420.23051870.16973985X-RAY DIFFRACTION98
2.5842-2.68760.20442430.16123971X-RAY DIFFRACTION98
2.6876-2.80990.21351820.16173941X-RAY DIFFRACTION97
2.8099-2.9580.18111530.16094102X-RAY DIFFRACTION99
2.958-3.14330.20762250.15733992X-RAY DIFFRACTION99
3.1433-3.38590.19882100.15163976X-RAY DIFFRACTION97
3.3859-3.72650.16391890.1413971X-RAY DIFFRACTION97
3.7265-4.26530.17151390.13853996X-RAY DIFFRACTION96
4.2653-5.37210.18992170.14453957X-RAY DIFFRACTION98
5.3721-42.48280.17462190.16623960X-RAY DIFFRACTION97

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