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- PDB-4kmc: Structure analysis of M. Tuberculosis rRNA transcriptional regula... -

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Basic information

Entry
Database: PDB / ID: 4kmc
TitleStructure analysis of M. Tuberculosis rRNA transcriptional regulator CarD and its interaction with T. Aquaticus RNA polymerase-BETA1 domain
ComponentsRNA polymerase-binding transcription factor CarD
KeywordsTRANSCRIPTION / UNKNOWN FOLD / rRNA TRANSCRIPTIONAL REGULATOR / RNA POLYMERASE BETA1 DOMAIN
Function / homology
Function and homology information


regulation of growth rate / stringent response / rRNA transcription
Similarity search - Function
CarD-like, C-terminal domain / : / CarD, C-terminal domain / CarD-like, C-terminal domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase-binding transcription factor CarD / RNA polymerase-binding transcription factor CarD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsGangwar, S.P. / Meena, S.R. / Saxena, A.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of the carboxy-terminal domain of Mycobacterium tuberculosis CarD protein: an essential rRNA transcriptional regulator.
Authors: Gangwar, S.P. / Meena, S.R. / Saxena, A.K.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Database references / Category: citation / reflns_shell
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _reflns_shell.Rmerge_I_obs
Revision 1.2Mar 20, 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: RNA polymerase-binding transcription factor CarD


Theoretical massNumber of molelcules
Total (without water)8,8831
Polymers8,8831
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA polymerase-binding transcription factor CarD

A: RNA polymerase-binding transcription factor CarD


Theoretical massNumber of molelcules
Total (without water)17,7662
Polymers17,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1900 Å2
ΔGint-13 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.957, 60.957, 59.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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Components

#1: Protein RNA polymerase-binding transcription factor CarD


Mass: 8883.027 Da / Num. of mol.: 1 / Fragment: C terminal domain, UNP residues 83-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: carD, MT3689, Rv3583c / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53568, UniProt: P9WJG3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 4000, 0.2M Magnisium sulphate, 30% Ethylene Glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→50.3 Å / Num. obs: 6559 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 28.6 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 7.9 / Num. unique all: 334 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→30.479 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7555 / SU ML: 0.22 / σ(F): 1.35 / σ(I): 0 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 304 4.66 %RANDOM
Rwork0.2185 ---
all0.22 6559 --
obs0.22 6522 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.11 Å2 / Biso mean: 49.7209 Å2 / Biso min: 29.49 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 0 15 631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007620
X-RAY DIFFRACTIONf_angle_d0.866833
X-RAY DIFFRACTIONf_chiral_restr0.05196
X-RAY DIFFRACTIONf_plane_restr0.003108
X-RAY DIFFRACTIONf_dihedral_angle_d13.509237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.146-2.70350.27311580.212130283186
2.7035-30.48160.24761460.2231903336
Refinement TLS params.Method: refined / Origin x: 8.4746 Å / Origin y: -3.078 Å / Origin z: 7.8578 Å
111213212223313233
T0.3682 Å20.0271 Å2-0.0276 Å2-0.3574 Å2-0.0083 Å2--0.2735 Å2
L2.0372 °20.5259 °20.045 °2-1.5962 °20.5531 °2--1.1779 °2
S-0.2638 Å °0.2749 Å °-0.0264 Å °-0.3059 Å °0.3113 Å °-0.1524 Å °-0.1206 Å °0.0442 Å °-0.0638 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA83 - 161
2X-RAY DIFFRACTION1allA1 - 215

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