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- PDB-5uh7: Crystal structure of beta'MtbSI of Mycobacterium tuberculosis RNA... -

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Basic information

Entry
Database: PDB / ID: 5uh7
TitleCrystal structure of beta'MtbSI of Mycobacterium tuberculosis RNA polymerase
ComponentsDNA-directed RNA polymerase subunit beta'
KeywordsTRANSCRIPTION / RNA polymerase complex / DNA / RNA
Function / homology
Function and homology information


Antimicrobial action and antimicrobial resistance in Mtb / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 ...DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.199 Å
AuthorsLin, W. / Das, K. / Feng, Y. / Ebright, R.H.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.
Authors: Lin, W. / Mandal, S. / Degen, D. / Liu, Y. / Ebright, Y.W. / Li, S. / Feng, Y. / Zhang, Y. / Mandal, S. / Jiang, Y. / Liu, S. / Gigliotti, M. / Talaue, M. / Connell, N. / Das, K. / Arnold, E. / Ebright, R.H.
History
DepositionJan 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 6, 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
A: DNA-directed RNA polymerase subunit beta'
B: DNA-directed RNA polymerase subunit beta'


Theoretical massNumber of molelcules
Total (without water)39,0252
Polymers39,0252
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-4 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.753, 97.500, 53.741
Angle α, β, γ (deg.)90.000, 93.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 19512.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rpoC, Rv0668, MTCI376.07c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGY7, DNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium citrate tribasic dihydrate, pH 5.5, and 22% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21229 / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.04 / Rrim(I) all: 0.086 / Χ2: 0.841 / Net I/σ(I): 11 / Num. measured all: 91896
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.283.50.50820650.7910.3020.5930.86996.8
2.28-2.373.80.44421080.8880.2560.5140.86299.3
2.37-2.484.10.38221150.930.2120.4380.87599.8
2.48-2.614.40.30721250.9580.1640.3490.892100
2.61-2.774.60.25121390.9750.1290.2830.862100
2.77-2.994.60.16121290.9850.0830.1820.86100
2.99-3.294.60.10421240.9870.0540.1170.879100
3.29-3.764.60.07121410.9920.0380.0810.876100
3.76-4.744.60.05821380.9940.0310.0660.892100
4.74-504.40.04321450.9940.0240.0490.54997.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
RefinementResolution: 2.199→36.08 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 3252 10.03 %
Rwork0.2198 --
obs0.2225 32409 77.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.98 Å2 / Biso mean: 49.2648 Å2 / Biso min: 19.16 Å2
Refinement stepCycle: final / Resolution: 2.199→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 0 43 2196
Biso mean---42.88 -
Num. residues----264

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