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- PDB-1g0i: CRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE... -

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Basic information

Entry
Database: PDB / ID: 1g0i
TitleCRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE-FRUCTOSE 1,6 BISPHOSPHATASE
ComponentsINOSITOL MONOPHOSPHATASEInositol-phosphate phosphatase
KeywordsHYDROLASE / HOMODIMER / COMPLEXED WITH Mn2+ / inositol / and phosphate
Function / homology
Function and homology information


inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / carbohydrate metabolic process / signal transduction / metal ion binding
Similarity search - Function
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 ...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
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / : / PHOSPHATE ION / Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsJohnson, K.A. / Chen, L. / Yang, H. / Roberts, M.F. / Stec, B.
Citation
Journal: Biochemistry / Year: 2001
Title: Crystal structure and catalytic mechanism of the MJ0109 gene product: a bifunctional enzyme with inositol monophosphatase and fructose 1,6-bisphosphatase activities.
Authors: Johnson, K.A. / Chen, L. / Yang, H. / Roberts, M.F. / Stec, B.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: MJ0109 is an Enzyme that is Both an Inositol Monophosphatse and the 'Missing' Archaeal Fructose-1,6-Bisphosphatase
Authors: Stec, B. / Yang, H. / Johnson, K.A. / Chen, L. / Roberts, M.F.
History
DepositionOct 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
B: INOSITOL MONOPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,10412
Polymers57,2242
Non-polymers88010
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.02, 78.45, 130.05
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chain A and B

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Components

#1: Protein INOSITOL MONOPHOSPHATASE / Inositol-phosphate phosphatase / MJ0109 GENE PRODUCT


Mass: 28611.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: PET23A+ / Production host: Escherichia coli (E. coli) / References: UniProt: Q57573, inositol-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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL / Inositol


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Comment: neurotransmitter, hormone*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 8000, sodium chloride, manganese chloride, TRIS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlenzyme1drop
211 %(w/v)PEG80001drop
350 mMTris-HCl1drop
4100 mM1dropNaCl
510 mM1dropCaCl2
611-15 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jul 26, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 26181 / Num. obs: 25134 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1 / Num. unique all: 2758 / % possible all: 90.5
Reflection
*PLUS
Num. obs: 26224 / % possible obs: 97.4 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 94.5 %

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
SDMSdata reduction
SDMSdata scaling
RefinementStarting model: 1AWB

1awb


Resolution: 2.4→12 Å / Num. parameters: 16495 / Num. restraintsaints: 16934 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: conjugated gradient least squares
RfactorNum. reflection% reflectionSelection details
Rfree0.339 1308 5 %every 20th reflection
Rwork0.251 ---
all0.259 24858 --
obs0.251 24858 94.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 2.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 40 48 4124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0.105
X-RAY DIFFRACTIONs_from_restr_planes0.294
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 12 Å / σ(F): 0 / Rfactor all: 0.251 / Rfactor obs: 0.192 / Rfactor Rfree: 0.322
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 0.021

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