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- PDB-6b62: IMPase (AF2372) with 400 mM Glutamate -

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Basic information

Entry
Database: PDB / ID: 6b62
TitleIMPase (AF2372) with 400 mM Glutamate
ComponentsFructose-1,6-bisphosphatase/inositol-1-monophosphatase
KeywordsHYDROLASE / Osmolyte binding protein / inositol monophosphatase
Function / homology
Function and homology information


inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / 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 ...Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / 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
GLUTAMIC ACID / Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsGoldstein, R.I. / Roberts, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-91-ER20025 United States
CitationJournal: To Be Published
Title: Osmolyte binding capacity of a dual action IMPase/FBPase (AF2372)
Authors: Goldstein, R.I. / Roberts, M.
History
DepositionOct 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
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.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.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: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
B: Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,94021
Polymers56,0062
Non-polymers1,93519
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-131 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.509, 89.509, 103.139
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fructose-1,6-bisphosphatase/inositol-1-monophosphatase / FBPase/IMPase / Inositol-1-phosphatase / I-1-Pase


Mass: 28002.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: suhB, AF_2372 / Production host: Escherichia coli (E. coli)
References: UniProt: O30298, fructose-bisphosphatase, inositol-phosphate phosphatase

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Non-polymers , 5 types, 351 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 4.26 Å3/Da / Density % sol: 71.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM myo inositol 400 mM Glutamate 25% PEG 3350 200 mM Potassium Sulfate 4 mM Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.75 Å / Num. obs: 62169 / % possible obs: 99.98 % / Redundancy: 5.8 % / Net I/σ(I): 4.244

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LBV

1lbv


Resolution: 2.003→44.75 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 16.99
RfactorNum. reflection% reflection
Rfree0.1715 3149 5.07 %
Rwork0.1611 --
obs0.1617 62169 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 122 332 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.054229
X-RAY DIFFRACTIONf_angle_d1.2235729
X-RAY DIFFRACTIONf_dihedral_angle_d14.6631621
X-RAY DIFFRACTIONf_chiral_restr0.075607
X-RAY DIFFRACTIONf_plane_restr0.006750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0029-2.03420.21671590.21622700X-RAY DIFFRACTION100
2.0342-2.06760.24371310.21462713X-RAY DIFFRACTION100
2.0676-2.10320.22021300.20782667X-RAY DIFFRACTION100
2.1032-2.14150.21411210.20982684X-RAY DIFFRACTION100
2.1415-2.18260.22421530.19722707X-RAY DIFFRACTION100
2.1826-2.22720.19371650.18442640X-RAY DIFFRACTION100
2.2272-2.27560.20531150.18532711X-RAY DIFFRACTION100
2.2756-2.32860.16821540.17582642X-RAY DIFFRACTION100
2.3286-2.38680.17621650.16722696X-RAY DIFFRACTION100
2.3868-2.45130.19261420.16782673X-RAY DIFFRACTION100
2.4513-2.52340.16051510.16222680X-RAY DIFFRACTION100
2.5234-2.60490.18111390.16212668X-RAY DIFFRACTION100
2.6049-2.6980.17331440.15242655X-RAY DIFFRACTION100
2.698-2.8060.16661620.14692690X-RAY DIFFRACTION100
2.806-2.93370.17411370.14912685X-RAY DIFFRACTION100
2.9337-3.08830.15841560.15012704X-RAY DIFFRACTION100
3.0883-3.28170.17361140.15462690X-RAY DIFFRACTION100
3.2817-3.5350.15631330.14692701X-RAY DIFFRACTION100
3.535-3.89060.14771480.13412696X-RAY DIFFRACTION100
3.8906-4.45310.12711500.13032668X-RAY DIFFRACTION100
4.4531-5.60870.16441420.15842680X-RAY DIFFRACTION100
5.6087-44.76570.20861380.19482670X-RAY DIFFRACTION100

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