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- PDB-4xax: Crystal structure of Thermus thermophilus CarD in complex with th... -

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Basic information

Entry
Database: PDB / ID: 4xax
TitleCrystal structure of Thermus thermophilus CarD in complex with the Thermus aquaticus RNA polymerase beta1 domain
Components
  • CarD
  • DNA-directed RNA polymerase subunit beta domain 1
KeywordsTranscription Regulator
Function / homology
Function and homology information


rRNA transcription / DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / DNA-templated transcription / DNA binding
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, 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 / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CarD-like/TRCF RNAP-interacting domain-containing protein / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsChen, J. / Bae, B. / Campbell, E.A. / Darst, S.A.
CitationJournal: Elife / Year: 2015
Title: CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.
Authors: Bae, B. / Chen, J. / Davis, E. / Leon, K. / Darst, S.A. / Campbell, E.A.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Data collection
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit beta domain 1
B: CarD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4267
Polymers38,1162
Non-polymers3105
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint14 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.321, 149.321, 52.256
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

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Components

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


Mass: 20545.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: beta1 domain (UNP residues 17-139 and 334-395) / Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: rpoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase
#2: Protein CarD


Mass: 17570.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0168 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLX5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Ammonium sulfate, sodium acetate, ethylene gycol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.41
ReflectionResolution: 2.4→50 Å / Num. obs: 22705 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Χ2: 1.033 / Net I/av σ(I): 25.176 / Net I/σ(I): 9.9 / Num. measured all: 138939
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.404-2.495.80.96122590.685100
2.49-2.596.20.73822560.706100
2.59-2.76.20.52922410.728100
2.7-2.856.20.3522390.756100
2.85-3.026.20.21922630.803100
3.02-3.266.20.12922540.842100
3.26-3.586.20.07622770.968100
3.58-4.16.10.0622681.556100
4.1-5.1760.0523042.011100
5.17-505.90.03423441.26999.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L5G, 3MLQ

4l5g

3mlq


Resolution: 2.404→49.323 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.74 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1803 1161 5.11 %
Rwork0.1563 21498 -
obs0.1615 22705 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.9 Å2 / Biso mean: 60.0647 Å2 / Biso min: 15.6 Å2
Refinement stepCycle: final / Resolution: 2.404→49.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 20 76 2753
Biso mean--49.77 52.81 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012725
X-RAY DIFFRACTIONf_angle_d1.1823677
X-RAY DIFFRACTIONf_chiral_restr0.045403
X-RAY DIFFRACTIONf_plane_restr0.006486
X-RAY DIFFRACTIONf_dihedral_angle_d17.021039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4047-2.5140.29151510.251926532804
2.514-2.64630.25621520.232126682820
2.6463-2.81180.27531490.215826522801
2.8118-3.02840.20181430.194226662809
3.0284-3.33230.21131330.190626782811
3.3323-3.81230.17971410.168426902831
3.8123-4.79520.15591500.125727202870
4.7952-22.21960.16171420.128627712913

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