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- PDB-4l5g: Crystal structure of Thermus thermophilus CarD -

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Basic information

Entry
Database: PDB / ID: 4l5g
TitleCrystal structure of Thermus thermophilus CarD
ComponentsCarD
KeywordsTRANSCRIPTION / Transcription regulator / RNA polymerase
Function / homology
Function and homology information


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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Thrombin, subunit H / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CarD-like/TRCF RNAP-interacting domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3902 Å
AuthorsSrivastava, D.B. / Westblade, L.F. / Campbell, E.A. / Darst, S.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure and function of CarD, an essential mycobacterial transcription factor.
Authors: Srivastava, D.B. / Leon, K. / Osmundson, J. / Garner, A.L. / Weiss, L.A. / Westblade, L.F. / Glickman, M.S. / Landick, R. / Darst, S.A. / Stallings, C.L. / Campbell, E.A.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CarD
B: CarD


Theoretical massNumber of molelcules
Total (without water)37,0882
Polymers37,0882
Non-polymers00
Water1,72996
1
A: CarD


Theoretical massNumber of molelcules
Total (without water)18,5441
Polymers18,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CarD


Theoretical massNumber of molelcules
Total (without water)18,5441
Polymers18,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.128, 136.085, 104.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-234-

HOH

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Components

#1: Protein CarD


Mass: 18543.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: CarD, TTHA0168 / Plasmid: Tth_pET_SUMO_CarD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLX5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, pH 6.5, 6% ethylene glycol, 30% (v/v) 1,3-butanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.39→27.862 Å / Num. all: 40964 / Num. obs: 40936 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 %
Reflection shellResolution: 2.39→2.49 Å / Redundancy: 4.2 % / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3902→27.862 Å / SU ML: 0.69 / σ(F): 1.06 / Phase error: 25.47 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2297 2080 5.08 %
Rwork0.2003 --
all0.2018 40964 -
obs0.2018 40928 99.55 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.308 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.1289 Å2-0 Å2-0 Å2
2---16.1418 Å20 Å2
3----5.987 Å2
Refinement stepCycle: LAST / Resolution: 2.3902→27.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 0 96 2626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052641
X-RAY DIFFRACTIONf_angle_d0.8723592
X-RAY DIFFRACTIONf_dihedral_angle_d15.3751026
X-RAY DIFFRACTIONf_chiral_restr0.056387
X-RAY DIFFRACTIONf_plane_restr0.004479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3902-2.44580.37591310.3062456X-RAY DIFFRACTION95
2.4458-2.50690.36661590.27692629X-RAY DIFFRACTION100
2.5069-2.57470.26151290.26752560X-RAY DIFFRACTION100
2.5747-2.65040.30861280.24462595X-RAY DIFFRACTION100
2.6504-2.73590.24121240.23142629X-RAY DIFFRACTION100
2.7359-2.83360.28871490.24282593X-RAY DIFFRACTION100
2.8336-2.94690.33471760.25022552X-RAY DIFFRACTION100
2.9469-3.08080.27281390.23252621X-RAY DIFFRACTION100
3.0808-3.2430.27931290.20652616X-RAY DIFFRACTION100
3.243-3.44590.23651410.21672576X-RAY DIFFRACTION100
3.4459-3.71140.24811240.20392628X-RAY DIFFRACTION100
3.7114-4.08380.20811550.18512592X-RAY DIFFRACTION100
4.0838-4.67240.15981410.14972593X-RAY DIFFRACTION100
4.6724-5.87760.21891400.18312597X-RAY DIFFRACTION100
5.8776-27.86350.15861150.17322611X-RAY DIFFRACTION99
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)
12.1250.12010.86061.8229-0.3722.06050.3299-0.0498-0.5794-0.4823-0.10690.39370.97380.2055-0.04050.95130.2814-0.20010.4743-0.00860.622813.650513.595930.972
21.3198-0.52370.67752.7063-0.0732.19440.0269-0.09790.1312-0.2060.0449-0.22950.26610.328-0.05990.25660.0974-0.03210.4465-0.0530.392811.142638.607722.6371
32.4530.30341.5562.11120.56582.08980.2097-0.37410.14420.3259-0.0638-0.0178-0.435-0.5142-0.13040.86470.2198-0.06340.5087-0.00110.510922.445316.162642.3299
41.25561.04871.18314.46541.72532.02260.00650.2512-0.01440.26850.2434-0.0939-0.14350.2898-0.15940.3735-0.00970.05790.4176-0.03070.291339.8713-4.23541.3169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resseq 3:62
2X-RAY DIFFRACTION2chain 'A' and resseq 63:164
3X-RAY DIFFRACTION3chain 'B' and resseq 0:62
4X-RAY DIFFRACTION4chain 'B' and resseq 63:160

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