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- PDB-1l2f: Crystal structure of NusA from Thermotoga maritima: a structure-b... -

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Basic information

Entry
Database: PDB / ID: 1l2f
TitleCrystal structure of NusA from Thermotoga maritima: a structure-based role of the N-terminal domain
ComponentsN utilization substance protein A
KeywordsTRANSCRIPTION / NusA / OB fold KH domain / RNA polymerase / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
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 / K homology domain-like, alpha/beta / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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, SAD / Resolution: 2.5 Å
AuthorsShin, D.H. / Nguyen, H.H. / Jancarik, J. / Yokota, H. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Biochemistry / Year: 2003
Title: Crystal structure of NusA from Thermotoga maritima and functional implication of the N-terminal domain.
Authors: Shin, D.H. / Nguyen, H.H. / Jancarik, J. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionFeb 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N utilization substance protein A


Theoretical massNumber of molelcules
Total (without water)41,1461
Polymers41,1461
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.191, 116.191, 64.631
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
11A-2152-

HOH

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Components

#1: Protein N utilization substance protein A / NUSA


Mass: 41146.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS.RARE / References: UniProt: Q9X298
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31 mMEDTA1drop
40.2 M1dropNaCl
55 %glycerol1drop
62 %PEG4001reservoir
72.0 Mammonium sulfate1reservoir
80.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97923,0.97904,0.95372
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2001
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979041
30.953721
ReflectionResolution: 2.5→43 Å / Num. all: 16004 / Num. obs: 15964 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.1 Å2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 43 Å / Num. obs: 29536 / Redundancy: 10.5 % / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 96.8 % / Redundancy: 8.3 % / Num. unique obs: 1408 / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD, SAD / Resolution: 2.5→29.05 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 275235.29 / Data cutoff high rms absF: 275235.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1578 10 %RANDOM
Rwork0.223 ---
all0.23 15829 --
obs-15829 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.9517 Å2 / ksol: 0.370057 e/Å3
Displacement parametersBiso mean: 60.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.4 Å20 Å20 Å2
2---7.4 Å20 Å2
3---14.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 0 219 2886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.34
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 239 9.5 %
Rwork0.299 2287 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.34

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