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- PDB-6b61: IMPase (AF2372) with 25 mM Asp -

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Basic information

Entry
Database: PDB / ID: 6b61
TitleIMPase (AF2372) with 25 mM Asp
ComponentsFructose-1,6-bisphosphatase/inositol-1-monophosphatase
KeywordsHYDROLASE / Osmolyte binding protein / inositol monophosphatase
Function / homology
Function and homology information


inositol-phosphate phosphatase / inositol monophosphate 1-phosphatase activity / inositol metabolic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / signal transduction / 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
ASPARTIC ACID / PHOSPHATE ION / Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)57,57516
Polymers56,0062
Non-polymers1,57014
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-48 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.619, 89.619, 102.375
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Fructose-1,6-bisphosphatase/inositol-1-monophosphatase


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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 4.24 Å3/Da / Density % sol: 70.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM myo inositol 400 mM Aspartate 12 % PEG 3350 200 mM Potassium Sulfate 100 mM Magnesium Chloride 100 mM HEPES pH7.0

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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: Nov 18, 2010
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: 2.6 % / Net I/σ(I): 2.161

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LVB

1lvb


Resolution: 2.7→42.731 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.9
RfactorNum. reflection% reflection
Rfree0.225 1252 4.98 %
Rwork0.1786 --
obs0.1809 25139 99.51 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 34.576 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4561 Å20 Å2-0 Å2
2--1.4561 Å20 Å2
3----2.9122 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 102 150 4184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084100
X-RAY DIFFRACTIONf_angle_d1.0765514
X-RAY DIFFRACTIONf_dihedral_angle_d14.7261546
X-RAY DIFFRACTIONf_chiral_restr0.072596
X-RAY DIFFRACTIONf_plane_restr0.004734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80810.30551300.23592658X-RAY DIFFRACTION100
2.8081-2.93590.29311590.23172661X-RAY DIFFRACTION100
2.9359-3.09060.30411350.21612668X-RAY DIFFRACTION100
3.0906-3.28420.23391510.18322619X-RAY DIFFRACTION99
3.2842-3.53770.18511280.16692669X-RAY DIFFRACTION99
3.5377-3.89350.23031470.15822659X-RAY DIFFRACTION99
3.8935-4.45640.19181270.15032644X-RAY DIFFRACTION99
4.4564-5.61250.1891370.15362662X-RAY DIFFRACTION100
5.6125-42.73620.21731380.19972647X-RAY DIFFRACTION99

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