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- PDB-4kbm: Structure of the Mtb CarD/RNAP Beta subunit B1-B2 domains complex -

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Basic information

Entry
Database: PDB / ID: 4kbm
TitleStructure of the Mtb CarD/RNAP Beta subunit B1-B2 domains complex
Components
  • DNA-directed RNA polymerase subunit beta
  • RNA polymerase-binding transcription factor CarD
KeywordsTRANSFERASE/TRANSCRIPTION / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Tudor / DNA-dependent RNA polymerase / transcription regulator / protein-protein complex / CarD / DNA / sigma factor / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


regulation of growth rate / cell wall / Antimicrobial action and antimicrobial resistance in Mtb / stringent response / rRNA transcription / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity ...regulation of growth rate / cell wall / Antimicrobial action and antimicrobial resistance in Mtb / stringent response / rRNA transcription / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to antibiotic / DNA-templated transcription / DNA binding / plasma membrane / cytosol
Similarity search - Function
CarD-like, C-terminal domain / CarD-like, C-terminal domain / : / : / CarD, 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 / Thrombin, subunit H - #170 ...CarD-like, C-terminal domain / CarD-like, C-terminal domain / : / : / CarD, 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 / Thrombin, subunit H - #170 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase beta subunit, bacterial-type / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Thrombin, subunit H / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA polymerase-binding transcription factor CarD / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta / RNA polymerase-binding transcription factor CarD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1146 Å
AuthorsGulten, G. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2013
Title: Structure of the Mtb CarD/RNAP beta-Lobes Complex Reveals the Molecular Basis of Interaction and Presents a Distinct DNA-Binding Domain for Mtb CarD.
Authors: Gulten, G. / Sacchettini, J.C.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: RNA polymerase-binding transcription factor CarD


Theoretical massNumber of molelcules
Total (without water)64,2002
Polymers64,2002
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.152, 128.889, 225.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 46266.324 Da / Num. of mol.: 1 / Fragment: B1 and B2 domains of Mtb RNAP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0695, MTCI376.08c, rpoB, Rv0667 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS
References: UniProt: P0A680, UniProt: P9WGY9*PLUS, DNA-directed RNA polymerase
#2: Protein RNA polymerase-binding transcription factor CarD


Mass: 17933.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: carD, MT3689, Rv3583c / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O53568, UniProt: P9WJG3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14% PEG 3350, 2% tacsimate pH 5.0, 0.1 M sodium citrate tribasic dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MAR 300 / Detector: CCD / Date: Jun 9, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.11→37.59 Å / Num. all: 40844 / Num. obs: 40844 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.11→2.21 Å / Mean I/σ(I) obs: 2.03 / Num. unique all: 4675 / % possible all: 92

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXPhasermodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXPhaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KBJ

4kbj


Resolution: 2.1146→37.588 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 2055 5.04 %Random
Rwork0.2079 ---
all0.2095 40748 --
obs0.2095 40748 97.97 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.559 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6012 Å2-0 Å20 Å2
2---3.4405 Å20 Å2
3---4.0417 Å2
Refinement stepCycle: LAST / Resolution: 2.1146→37.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 0 305 4508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054268
X-RAY DIFFRACTIONf_angle_d0.8725770
X-RAY DIFFRACTIONf_dihedral_angle_d14.2761617
X-RAY DIFFRACTIONf_chiral_restr0.059663
X-RAY DIFFRACTIONf_plane_restr0.004751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1146-2.16380.31191200.27182215X-RAY DIFFRACTION85
2.1638-2.21790.29321300.25342587X-RAY DIFFRACTION99
2.2179-2.27790.29271310.2422573X-RAY DIFFRACTION100
2.2779-2.34490.27331390.23282600X-RAY DIFFRACTION100
2.3449-2.42060.25211430.23042555X-RAY DIFFRACTION100
2.4206-2.50710.2711430.22072623X-RAY DIFFRACTION100
2.5071-2.60740.28681400.2262573X-RAY DIFFRACTION100
2.6074-2.72610.28451200.23182650X-RAY DIFFRACTION100
2.7261-2.86980.30251330.22872623X-RAY DIFFRACTION100
2.8698-3.04950.27921410.22372588X-RAY DIFFRACTION100
3.0495-3.28480.24021150.2132652X-RAY DIFFRACTION99
3.2848-3.61510.22881400.20012585X-RAY DIFFRACTION98
3.6151-4.13770.20741360.18622579X-RAY DIFFRACTION97
4.1377-5.21080.18931560.16192566X-RAY DIFFRACTION96
5.2108-37.59360.22091680.20582724X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1422-0.71961.00971.4838-0.00161.6877-0.0423-0.12030.0235-0.1048-0.0237-0.0311-0.06850.04270.01980.07770.0179-0.0230.1676-0.03070.0997-10.1388-4.468439.7123
20.4729-0.6321-0.21351.70150.36380.2404-0.0101-0.1019-0.0939-0.0446-0.06870.0390.0766-0.06060.03390.0877-0.0105-0.01880.14630.00840.1579-9.5773-28.838133.399
31.3749-1.4717-0.38773.07810.15260.15140.0283-0.21250.12650.0860.1574-0.79840.09550.0301-0.1870.13160.01240.00310.18410.0080.36293.8151-34.265334.3786
45.2176-0.85420.61935.5468-0.27014.824-0.05390.27410.069-0.48230.0562-0.2875-0.27220.1617-0.01630.1485-0.0033-0.0140.12450.02420.2051-33.07111.63117.1702
53.79680.00860.7592.6988-0.5657.2488-0.29780.06050.0230.288-0.07650.0438-0.10830.38540.38580.38470.12670.10860.28480.04370.2496-43.921216.4987-2.2026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -5:128)
2X-RAY DIFFRACTION2chain 'A' and (resseq 129:325)
3X-RAY DIFFRACTION3chain 'A' and (resseq 328:379)
4X-RAY DIFFRACTION4chain 'B' and (resseq 2:58)
5X-RAY DIFFRACTION5chain 'B' and (resseq 63:145)

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