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- PDB-1lbv: Crystal Structure of apo-form (P21) of dual activity FBPase/IMPas... -

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Basic information

Entry
Database: PDB / ID: 1lbv
TitleCrystal Structure of apo-form (P21) of dual activity FBPase/IMPase (AF2372) from Archaeoglobus fulgidus
Componentsfructose 1,6-bisphosphatase/inositol monophosphatase
KeywordsHYDROLASE / dual activity / FBPase / IMPase / archaeal phosphatase / apo-form
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
Fructose-1,6-bisphosphatase/inositol-1-monophosphatase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStieglitz, K.A. / Johnson, K.A. / Yang, H. / Roberts, M.F. / Seaton, B.A. / Head, J.F. / Stec, B.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of a dual activity IMPase/FBPase (AF2372) from Archaeoglobus fulgidus. The story of a mobile loop.
Authors: Stieglitz, K.A. / Johnson, K.A. / Yang, H. / Roberts, M.F. / Seaton, B.A. / Head, J.F. / Stec, B.
#1: 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.
History
DepositionApr 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Remark 999SEQUENCE THIS SEQUENCE IS ANNOTATED IN THE PIR ENTRY D69546 AS SUHB ANALOGUE, WHICH WAS BASED ON ...SEQUENCE THIS SEQUENCE IS ANNOTATED IN THE PIR ENTRY D69546 AS SUHB ANALOGUE, WHICH WAS BASED ON SEQUENCE HOMOLOGIES, NOT BIOCHEMICAL ASSAYS.

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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 monophosphatase
B: fructose 1,6-bisphosphatase/inositol monophosphatase


Theoretical massNumber of molelcules
Total (without water)56,0062
Polymers56,0062
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-11 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.812, 53.247, 82.154
Angle α, β, γ (deg.)90.00, 105.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein fructose 1,6-bisphosphatase/inositol monophosphatase / FBPase/IMPase


Mass: 28002.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF2372 / Production host: Escherichia coli (E. coli)
References: UniProt: O30298, fructose-bisphosphatase, inositol-phosphate phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, ammonium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Mdihydrogen ammonium phosphate1reservoir
230 %PEG33501reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2000
RadiationMonochromator: collimating mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 38204 / Num. obs: 37007 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3370 / % possible all: 86.2
Reflection
*PLUS
Num. obs: 35243 / % possible obs: 93.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 83.9 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.27

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DK4

1dk4


Resolution: 1.8→31.81 Å / Num. parameters: 16663 / Num. restraintsaints: 16078 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: SHELXL CONJUGATED GRADIENT
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1468 5 %RANDOM
Rwork0.203 ---
all0.215 37007 --
obs0.215 37007 97 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refinement stepCycle: LAST / Resolution: 1.8→31.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 0 233 4165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.034
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / % reflection Rfree: 4 % / Rfactor all: 0.215 / Rfactor obs: 0.203 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_bond_d / Dev ideal: 0.007

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