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- PDB-6ib7: Structure of wild type SuhB -

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Basic information

Entry
Database: PDB / ID: 6ib7
TitleStructure of wild type SuhB
ComponentsInositol-1-monophosphatase
KeywordsTRANSCRIPTION / SuhB / antitermiantion
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 / transcription antitermination factor activity, RNA binding / phosphatidylinositol phosphate biosynthetic process ...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 / transcription antitermination factor activity, RNA binding / phosphatidylinositol phosphate biosynthetic process / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.245 Å
AuthorsHuang, Y.H. / Loll, B. / Wahl, M.C.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis.
Authors: Huang, Y.H. / Said, N. / Loll, B. / Wahl, M.C.
History
DepositionNov 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: 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.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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: Inositol-1-monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7464
Polymers29,5381
Non-polymers2083
Water54030
1
A: Inositol-1-monophosphatase
hetero molecules

A: Inositol-1-monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4928
Polymers59,0752
Non-polymers4176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4470 Å2
ΔGint-24 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.718, 46.031, 72.915
Angle α, β, γ (deg.)90.00, 125.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Inositol-1-monophosphatase / Inositol-1-phosphatase


Mass: 29537.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: suhB, ssyA, b2533, JW2517 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADG4, inositol-phosphate phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 0.1M Tris-HCl, pH 8.3, 12% PEG 8000,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 26, 2017
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.245→50 Å / Num. obs: 11994 / % possible obs: 97.2 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 10.7
Reflection shellResolution: 2.245→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1919 / CC1/2: 0.58 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFL

2qfl


Resolution: 2.245→36.975 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.52
RfactorNum. reflection% reflection
Rfree0.2605 581 5 %
Rwork0.2148 --
obs0.2172 11611 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.245→36.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 13 30 2017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052051
X-RAY DIFFRACTIONf_angle_d0.7362781
X-RAY DIFFRACTIONf_dihedral_angle_d10.3541660
X-RAY DIFFRACTIONf_chiral_restr0.047310
X-RAY DIFFRACTIONf_plane_restr0.003368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2451-2.4710.41450.3312741X-RAY DIFFRACTION97
2.471-2.82840.35061440.27212744X-RAY DIFFRACTION98
2.8284-3.5630.28911460.23682765X-RAY DIFFRACTION98
3.563-36.97980.21521460.1812780X-RAY DIFFRACTION97

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