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- PDB-2qfl: Structure of SuhB: Inositol monophosphatase and extragenic suppre... -

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Basic information

Entry
Database: PDB / ID: 2qfl
TitleStructure of SuhB: Inositol monophosphatase and extragenic suppressor from E. coli
ComponentsInositol-1-monophosphatase
KeywordsHYDROLASE / IMPase Extragenic suppressor / Dimerization
Function / homology
Function and homology information


glycerol-2-phosphatase activity / lithium ion binding / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / rRNA primary transcript binding / phosphatidylinositol phosphate biosynthetic process / transcription antitermination factor activity, RNA binding ...glycerol-2-phosphatase activity / lithium ion binding / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / rRNA primary transcript binding / phosphatidylinositol phosphate biosynthetic process / transcription antitermination factor activity, RNA binding / transcription antitermination / ribosome biogenesis / magnesium ion binding / signal transduction / cytosol / cytoplasm
Similarity search - Function
Inositol monophosphatase SuhB-like / Inositol monophosphatase / 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 ...Inositol monophosphatase SuhB-like / Inositol monophosphatase / 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
ACETATE ION / ETHYL ACETATE / Nus factor SuhB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, Y. / Stieglitz, K.A. / Bubunenko, M. / Court, D. / Stec, B. / Roberts, M.F.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The structure of the R184A mutant of the inositol monophosphatase encoded by suhB and implications for its functional interactions in Escherichia coli.
Authors: Wang, Y. / Stieglitz, K.A. / Bubunenko, M. / Court, D.L. / Stec, B. / Roberts, M.F.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol-1-monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2683
Polymers29,1211
Non-polymers1472
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.767, 45.447, 71.758
Angle α, β, γ (deg.)90.00, 125.43, 90.00
Int Tables number5
Space group name H-MC121
Detailsremains in monomer - dimer equilibrium crystal structure of the mutant is a dimer

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Components

#1: Protein Inositol-1-monophosphatase / IMPase / Inositol-1-phosphatase / I-1-Pase


Mass: 29120.980 Da / Num. of mol.: 1 / Mutation: R184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: suhB, ssyA / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0ADG4, inositol-phosphate phosphatase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EEE / ETHYL ACETATE / Ethyl acetate


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 20% PEG 3350, 0.2M ammonium acetate, 0.05M TRIS, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 11, 2006 / Details: Osmic blue confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→47 Å / Num. all: 15955 / Num. obs: 15115 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.1 / Num. unique all: 740 / % possible all: 36

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Hybrid of human and MJ IMPase

Resolution: 1.9→47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.536 / SU ML: 0.162 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.24 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28555 830 5.2 %RANDOM
Rwork0.20922 ---
obs0.21331 15113 94.97 %-
all-15113 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.195 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å2-1.58 Å2
2--0.35 Å20 Å2
3----3.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 4 96 2107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222051
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9522777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4495261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11123.68495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89515333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3691517
X-RAY DIFFRACTIONr_chiral_restr0.1380.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021573
X-RAY DIFFRACTIONr_nbd_refined0.2370.21017
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21393
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.215
X-RAY DIFFRACTIONr_mcbond_it1.2881.51339
X-RAY DIFFRACTIONr_mcangle_it2.08722074
X-RAY DIFFRACTIONr_scbond_it2.7843812
X-RAY DIFFRACTIONr_scangle_it4.2344.5703
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 25 -
Rwork0.274 439 -
obs-540 34.09 %

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