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- PDB-1k0r: Crystal Structure of Mycobacterium tuberculosis NusA -

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Basic information

Entry
Database: PDB / ID: 1k0r
TitleCrystal Structure of Mycobacterium tuberculosis NusA
ComponentsNusA
KeywordsTRANSCRIPTION / Two component arrangement / S1 domain / two K-homology domains. / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


peptidoglycan-based cell wall / transcription antitermination / DNA-templated transcription termination / DNA-binding transcription factor activity / RNA binding / plasma membrane / cytosol / cytoplasm
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 / RNA-binding domain, S1 ...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 / RNA-binding domain, S1 / K homology (KH) domain / Type-1 KH domain profile. / GMP Synthetase; Chain A, domain 3 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / K homology domain superfamily, prokaryotic type / 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 / Transcription termination/antitermination protein NusA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsGopal, B. / Haire, L.F. / Gamblin, S.J. / Dodson, E.J. / Lane, A.N. / Papavinasasundaram, K.G. / Colston, M.J. / Dodson, G. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the transcription elongation/anti-termination factor NusA from Mycobacterium tuberculosis at 1.7 A resolution.
Authors: Gopal, B. / Haire, L.F. / Gamblin, S.J. / Dodson, E.J. / Lane, A.N. / Papavinasasundaram, K.G. / Colston, M.J. / Dodson, G.
History
DepositionSep 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: NusA
B: NusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1206
Polymers79,7362
Non-polymers3844
Water7,116395
1
A: NusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9642
Polymers39,8681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1564
Polymers39,8681
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.987, 88.987, 180.208
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NusA


Mass: 39867.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Elongation/Anti-termination factor / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MTCY24A1, number Z95207.1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: P0A5M2, UniProt: P9WIV3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.86 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: Ammonium sulphate, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 291 K / Details: Gopal, B., (2001) Acta Crystallog., D57, 1187.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
21.1 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.009, 0.939
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
20.9391
ReflectionResolution: 1.7→20 Å / Num. all: 82725 / Num. obs: 82725 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.103 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3389 / Rsym value: 0.562 / % possible all: 78.2
Reflection
*PLUS
% possible obs: 91.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.103

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 7917 10.021 %random
Rwork0.2477 ---
all0.2692 79003 --
obs0.2692 79003 86.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.669 Å2-0.037 Å20 Å2
2--1.669 Å20 Å2
3----3.338 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4952 0 20 395 5367
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.11474
X-RAY DIFFRACTIONc_bond_d0.004653
LS refinement shellResolution: 1.7→1.71 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.4108 54 -
Rwork0.3743 --
obs-443 1.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.211 / Rfactor Rfree: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS

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