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- PDB-1hh2: Crystal structure of NusA from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1hh2
TitleCrystal structure of NusA from Thermotoga maritima
ComponentsN UTILIZATION SUBSTANCE PROTEIN A
KeywordsTRANSCRIPTION REGULATION / TERMINATION
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / DNA-binding transcription factor activity / RNA binding / cytosol
Similarity search - Function
N Utilization Substance Protein A; Chain:P; domain 4 / NusA, N-terminal domain / 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 / K homology (KH) domain ...N Utilization Substance Protein A; Chain:P; domain 4 / NusA, N-terminal domain / 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 / K homology (KH) domain / Type-1 KH domain profile. / GMP Synthetase; Chain A, domain 3 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / K homology domain superfamily, prokaryotic type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / K homology domain-like, alpha/beta / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusA
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsWorbs, M. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. / Wahl, M.C.
CitationJournal: Mol.Cell / Year: 2001
Title: An Extended RNA Binding Surface Through Arrayed S1 and Kh Domains in Transcription Factor Nusa
Authors: Worbs, M. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. / Wahl, M.C.
History
DepositionDec 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
P: N UTILIZATION SUBSTANCE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)37,9731
Polymers37,9731
Non-polymers00
Water6,431357
1
P: N UTILIZATION SUBSTANCE PROTEIN A

P: N UTILIZATION SUBSTANCE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)75,9472
Polymers75,9472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445-y-1,-x-1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)115.531, 115.531, 63.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11P-2036-

HOH

DetailsA HOMODIMERIC ASSEMBLY IS OBSERVED.

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Components

#1: Protein N UTILIZATION SUBSTANCE PROTEIN A / NUSA


Mass: 37973.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Gene: NUSA / Plasmid: PET 22 B(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X298
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 53 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / PH range low: 7.4 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium sulfate1reservoir
22-5 %PEG4001reservoir
3100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.950,0.98
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.981
ReflectionResolution: 2.1→15 Å / Num. obs: 12248 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.035
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 25817 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.5

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3192 -10 %
Rwork0.2439 --
obs0.2439 25560 99 %
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 0 357 3024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010946
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.65879
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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