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- PDB-1eyv: THE CRYSTAL STRUCTURE OF NUSB FROM MYCOBACTERIUM TUBERCULOSIS -

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Basic information

Entry
Database: PDB / ID: 1eyv
TitleTHE CRYSTAL STRUCTURE OF NUSB FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsN-UTILIZING SUBSTANCE PROTEIN B HOMOLOG
KeywordsTRANSCRIPTION / helical bundle / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / RNA binding / cytosol
Similarity search - Function
N-utilizing Substance Protein B Homolog; Chain A / NusB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Transcription antitermination protein NusB / Transcription antitermination protein NusB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsGopal, B. / Haire, L.F. / Cox, R.A. / Colston, M.J. / Major, S. / Brannigan, J.A. / Smerdon, S.J. / Dodson, G.G. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: The crystal structure of NusB from Mycobacterium tuberculosis.
Authors: Gopal, B. / Haire, L.F. / Cox, R.A. / Colston, M.J. / Major, S. / Brannigan, J.A. / Smerdon, S.J. / Dodson, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance-B (NusB) from Mycobacterium tuberculosis.
Authors: Gopal, B. / Cox, R.A. / Colston, M.J. / Dodson, G.G. / Smerdon, S.J. / Haire, L.F.
History
DepositionMay 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-UTILIZING SUBSTANCE PROTEIN B HOMOLOG
B: N-UTILIZING SUBSTANCE PROTEIN B HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7204
Polymers33,5302
Non-polymers1902
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-24 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.330, 63.540, 90.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein N-UTILIZING SUBSTANCE PROTEIN B HOMOLOG / NUSB PROTEIN


Mass: 16765.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: P95020, UniProt: P9WIV1*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 0.1 M Na HEPES buffer, pH 7.5, 2 % PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Temperature: 291 K
Details: Gopal, B., (2000) Acta Crystallogr., Sect.D, 56, 64.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir
30.1 MNa HEPES1reservoir
42 %PEG4001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSRS PX9.610.87
SYNCHROTRONESRF BM142
DetectorDate: May 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 1501196 / Num. obs: 34118 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.331 / Num. unique all: 1328 / % possible all: 75
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
ARPmodel building
REFMACrefinement
RefinementResolution: 1.6→15 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1700 -RANDOM
Rwork0.19 ---
all-45657 --
obs-32254 95.2 %-
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 10 291 2309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.4
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg

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