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- PDB-6b60: IMPase (AF2372) with 25 mM Glutamate -

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Basic information

Entry
Database: PDB / ID: 6b60
TitleIMPase (AF2372) with 25 mM Glutamate
ComponentsFructose-1,6-bisphosphatase/inositol-1-monophosphatase
KeywordsHYDROLASE / Osmolyte binding protein Inositol mono phosphatase
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
GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGoldstein, R.I. / Roberts, M.F.
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_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)57,18215
Polymers56,0062
Non-polymers1,17613
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-125 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.201, 89.201, 102.041
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 DSM 4304 (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, 81 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 4.18 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM myo-inositol 25 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: Oct 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→31.13 Å / Num. obs: 24763 / % possible obs: 99.42 % / Redundancy: 7 % / Net I/σ(I): 2.302

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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: 1LBV

1lbv


Resolution: 2.7→31.13 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.03
RfactorNum. reflection% reflection
Rfree0.2377 1730 6.99 %
Rwork0.1914 --
obs0.1947 24763 99.42 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 38.856 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.3535 Å20 Å2-0 Å2
2--8.3535 Å20 Å2
3----16.707 Å2
Refinement stepCycle: LAST / Resolution: 2.7→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 71 68 4071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144081
X-RAY DIFFRACTIONf_angle_d1.5755490
X-RAY DIFFRACTIONf_dihedral_angle_d16.0141545
X-RAY DIFFRACTIONf_chiral_restr0.075591
X-RAY DIFFRACTIONf_plane_restr0.008724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.77950.35991360.29491925X-RAY DIFFRACTION100
2.7795-2.86920.42441400.3641916X-RAY DIFFRACTION99
2.8692-2.97160.55821400.4331910X-RAY DIFFRACTION98
2.9716-3.09050.44971500.36191918X-RAY DIFFRACTION99
3.0905-3.2310.30541460.25151895X-RAY DIFFRACTION100
3.231-3.40120.28781440.22531941X-RAY DIFFRACTION100
3.4012-3.6140.23541400.18971924X-RAY DIFFRACTION100
3.614-3.89250.23521460.16131938X-RAY DIFFRACTION100
3.8925-4.28340.17671450.1381927X-RAY DIFFRACTION100
4.2834-4.90110.15471470.12491890X-RAY DIFFRACTION99
4.9011-6.1670.19231500.15971932X-RAY DIFFRACTION100
6.167-31.13180.17951460.15461917X-RAY DIFFRACTION100

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