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- PDB-1m1h: Crystal structure of Aquifex aeolicus N-utilization substance G (... -

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Basic information

Entry
Database: PDB / ID: 1m1h
TitleCrystal structure of Aquifex aeolicus N-utilization substance G (NusG), Space group I222
ComponentsTranscription antitermination protein nusG
KeywordsTRANSCRIPTION / Transcription termination / Antitermination / RNP motif / immunoglobulin fold / nucleic acid interaction / protein-protein interaction
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / cytosol
Similarity search - Function
N-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / NusG, N-terminal domain / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. ...N-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / NusG, N-terminal domain / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Alpha-Beta Plaits / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsSteiner, T. / Kaiser, J.T. / Marinkovic, S. / Huber, R. / Wahl, M.C.
CitationJournal: Embo J. / Year: 2002
Title: Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities
Authors: Steiner, T. / Kaiser, J.T. / Marinkovic, S. / Huber, R. / Wahl, M.C.
History
DepositionJun 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)28,0421
Polymers28,0421
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.1, 86.2, 108.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a monomer

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Components

#1: Protein Transcription antitermination protein nusG


Mass: 28041.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67757
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 4000, 2-Propanol, Sodium Chloride, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MMES/Tris1reservoirpH5.8
210 %PEG40001reservoir
320 %2-propanol1reservoir
40.1 M1reservoirNaCl
520 mMTris-HCl1droppH7.0
650 mM1dropNaCl
71 MDNA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: CCD / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 27602 / Num. obs: 27602 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rsym value: 0.074 / Net I/σ(I): 30
Reflection shellResolution: 1.95→2.05 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.504 / % possible all: 98.4
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.504

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
REFMACrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.95→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1380 -random
Rwork0.234 ---
all0.234 27602 --
obs0.234 27602 98.4 %-
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 0 296 1732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.42
X-RAY DIFFRACTIONo_bond_d0.006
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / Rfactor Rwork: 0.283

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