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- PDB-6ib8: Structure of a complex of SuhB and NusA AR2 domain -

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Basic information

Entry
Database: PDB / ID: 6ib8
TitleStructure of a complex of SuhB and NusA AR2 domain
Components
  • Inositol-1-monophosphatase
  • Transcription termination/antitermination protein NusA
KeywordsTRANSCRIPTION / SuhB / NusA AR2 domain / 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 / bacterial-type RNA polymerase core enzyme binding / rRNA primary transcript binding / 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 / bacterial-type RNA polymerase core enzyme binding / rRNA primary transcript binding / transcription antitermination factor activity, RNA binding / phosphatidylinositol phosphate biosynthetic process / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / protein complex oligomerization / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding / magnesium ion binding / signal transduction / RNA binding / cytosol / cytoplasm
Similarity search - Function
Inositol monophosphatase SuhB-like / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Transcription termination factor NusA, C-terminal duplication / Inositol monophosphatase, metal-binding site / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily ...Inositol monophosphatase SuhB-like / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Transcription termination factor NusA, C-terminal duplication / Inositol monophosphatase, metal-binding site / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / RNA-binding domain, S1 / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / Type-1 KH domain profile. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / 5' to 3' exonuclease, C-terminal subdomain / D-Maltodextrin-Binding Protein; domain 2 / DNA polymerase; domain 1 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusA / Nus factor SuhB / Transcription termination/antitermination protein NusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.646 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 1.1Oct 30, 2019Group: Data collection / 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol-1-monophosphatase
B: Inositol-1-monophosphatase
C: Transcription termination/antitermination protein NusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,24115
Polymers66,7473
Non-polymers1,49412
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-20 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.270, 95.540, 104.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 3 molecules ABC

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


Mass: 29537.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: suhB, ssyA, b2533, JW2517 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADG4, inositol-phosphate phosphatase
#2: Protein Transcription termination/antitermination protein NusA


Mass: 7671.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusA, ECs4050 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3SSP1, UniProt: P0AFF6*PLUS

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Non-polymers , 4 types, 275 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 5% (w/v) PEG 8000, 16% (v/v) PEG 300, 10% (v/v) glycerol

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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 6, 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: 1.646→50 Å / Num. obs: 78162 / % possible obs: 99.1 % / Redundancy: 5.5 % / CC1/2: 0.99 / Net I/σ(I): 15.2
Reflection shellResolution: 1.646→1.74 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 12069 / CC1/2: 0.36 / Rrim(I) all: 1.86 / % possible all: 95.7

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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, 1WCN

2qfl

1wcn


Resolution: 1.646→30.634 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.84
RfactorNum. reflection% reflection
Rfree0.219 2095 2.69 %
Rwork0.1815 --
obs0.1825 77933 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.646→30.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 67 263 4872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154932
X-RAY DIFFRACTIONf_angle_d1.0096693
X-RAY DIFFRACTIONf_dihedral_angle_d7.243936
X-RAY DIFFRACTIONf_chiral_restr0.081744
X-RAY DIFFRACTIONf_plane_restr0.006891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6458-1.68410.41871260.37644523X-RAY DIFFRACTION90
1.6841-1.72620.35241390.3165039X-RAY DIFFRACTION100
1.7262-1.77290.37431400.28685037X-RAY DIFFRACTION100
1.7729-1.8250.28981390.24525035X-RAY DIFFRACTION100
1.825-1.88390.24361390.22345050X-RAY DIFFRACTION100
1.8839-1.95130.25681400.21095063X-RAY DIFFRACTION100
1.9513-2.02940.24781390.18245044X-RAY DIFFRACTION100
2.0294-2.12170.19631400.16825072X-RAY DIFFRACTION100
2.1217-2.23350.20731400.16275063X-RAY DIFFRACTION100
2.2335-2.37340.22461400.16655081X-RAY DIFFRACTION100
2.3734-2.55660.19471420.16575122X-RAY DIFFRACTION100
2.5566-2.81370.20231410.16535109X-RAY DIFFRACTION100
2.8137-3.22050.19741410.17355127X-RAY DIFFRACTION100
3.2205-4.0560.21581430.1665168X-RAY DIFFRACTION99
4.056-30.63940.2031460.17885305X-RAY DIFFRACTION98

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