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- PDB-2cxc: Crystal structure of archaeal transcription termination factor NusA -

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Basic information

Entry
Database: PDB / ID: 2cxc
TitleCrystal structure of archaeal transcription termination factor NusA
ComponentsNusA
KeywordsTRANSCRIPTION / TRANSCRIPTION TERMINATION / RNA BINDING PROTEIN / ARCHAEAL NUSA / KH DOMAIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / RNA binding / cytosol
Similarity search - Function
Probable transcription termination protein NusA, archaeal / Transcription termination/antitermination protein NusA, bacterial / K homology (KH) domain / Type-1 KH domain profile. / GMP Synthetase; Chain A, domain 3 / K Homology domain / K homology RNA-binding domain / KH domain / K Homology domain, type 2 / K homology domain superfamily, prokaryotic type ...Probable transcription termination protein NusA, archaeal / Transcription termination/antitermination protein NusA, bacterial / K homology (KH) domain / Type-1 KH domain profile. / GMP Synthetase; Chain A, domain 3 / K Homology domain / K homology RNA-binding domain / KH domain / K Homology domain, type 2 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable transcription termination protein NusA
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsShibata, R. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Crystal structure and RNA-binding analysis of the archaeal transcription factor NusA
Authors: Shibata, R. / Bessho, Y. / Shinkai, A. / Nishimoto, M. / Fusatomi, E. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: NusA


Theoretical massNumber of molelcules
Total (without water)16,0701
Polymers16,0701
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.348, 100.348, 45.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein NusA / hypothetical protein APE1850


Mass: 16069.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YAU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.8
Details: PEG 3350, sodium acetate, pH 4.8, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A10.97885, 0.97920, 0.97300
SYNCHROTRONSPring-8 BL26B121
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 3, 2004
RIGAKU JUPITER 2102CCDOct 10, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)MADMx-ray1
2Si double crystalsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978851
20.97921
30.9731
411
ReflectionResolution: 1.9→50 Å / Num. obs: 18141 / % possible obs: 99.8 % / Redundancy: 7.3521 % / Rsym value: 0.061 / Net I/σ(I): 35.83
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.9713 / Num. unique all: 1790 / Rsym value: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→35.5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 658296.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: HEMIHEDRAL TWINNING. TWINNING OPERATOR IS (K,H,-L) AND THE TWINNING FRACTION IS 0.218. THE R-FACTOR IS 0.184 AND THE R-FREE IS 0.211 WHEN THIS TWINNING OPERATOR IS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1200 7.7 %RANDOM
Rwork0.1844 ---
obs-15498 99.5 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---1.27 Å20 Å2
3---2.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 0 54 1134
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071.5
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d22.12
X-RAY DIFFRACTIONc_improper_angle_d0.612.5
X-RAY DIFFRACTIONc_mcbond_it1.38
X-RAY DIFFRACTIONc_mcangle_it2.43
X-RAY DIFFRACTIONc_scbond_it2.23
X-RAY DIFFRACTIONc_scangle_it3.57
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.288 145 8.1 %
Rwork0.253 2347 -
obs-1754 99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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