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- PDB-3woe: Crystal structure of P23-45 gp39 (6-109) bound to Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 3woe
TitleCrystal structure of P23-45 gp39 (6-109) bound to Thermus thermophilus RNA polymerase beta-flap domain
Components
  • DNA-directed RNA polymerase subunit betaPolymerase
  • Putative uncharacterized protein
KeywordsTRANSFERASE/TRANSCRIPTION / Transcription / RNA polymerase / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function
SH3 type barrels. - #1250 / Thermus phage P23-45 gp39, N-terminal domain / RNA polymerase II, Rpb2 subunit, wall domain / 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 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit ...SH3 type barrels. - #1250 / Thermus phage P23-45 gp39, N-terminal domain / RNA polymerase II, Rpb2 subunit, wall domain / 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 / 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 / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Thermus phage P23-45 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 2.351 Å
AuthorsTagami, S. / Sekine, S. / Minakhin, L. / Esyunina, D. / Akasaka, R. / Shirouzu, M. / Kulbachinskiy, A. / Severinov, K. / Yokoyama, S.
CitationJournal: Genes Dev. / Year: 2014
Title: Structural basis for promoter specificity switching of RNA polymerase by a phage factor.
Authors: Tagami, S. / Sekine, S. / Minakhin, L. / Esyunina, D. / Akasaka, R. / Shirouzu, M. / Kulbachinskiy, A. / Severinov, K. / Yokoyama, S.
History
DepositionDec 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references

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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: Putative uncharacterized protein
C: DNA-directed RNA polymerase subunit beta
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)53,2854
Polymers53,2854
Non-polymers00
Water1,820101
1
A: DNA-directed RNA polymerase subunit beta
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,6422
Polymers26,6422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-6 kcal/mol
Surface area13090 Å2
MethodPISA
2
C: DNA-directed RNA polymerase subunit beta
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,6422
Polymers26,6422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-4 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.232, 99.232, 117.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 14481.525 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 703-830
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoB, TTHA1813 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#2: Protein Putative uncharacterized protein / gp39


Mass: 12160.743 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 4-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage P23-45 (virus) / Strain: Thermus phage P23-45 / Gene: gp39 (P23p39), P23p39 / Plasmid: pET-47b / Production host: Escherichia coli (E. coli) / References: UniProt: A7XX65
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / pH: 8
Details: 50mM Tris-HCl (pH 8.0), 12% PEG 8000, 8% 2-propanol, 3% 1,6-hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.978
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 24, 2012
RadiationMonochromator: LIQUID NITROGEN COOLED DOUBLE CRYSTAL, SI (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 24886 / % possible obs: 99.5 % / Observed criterion σ(I): 6.5 / Redundancy: 17.7 % / Rsym value: 0.14 / Net I/σ(I): 19.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacementSAD / Resolution: 2.351→49.616 Å / SU ML: 0.26 / σ(F): 1.97 / Phase error: 23.96 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_ PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2253 2380 5.14 %
Rwork0.1813 --
obs0.1836 24861 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.351→49.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 0 101 3831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083812
X-RAY DIFFRACTIONf_angle_d1.0625170
X-RAY DIFFRACTIONf_dihedral_angle_d15.3981486
X-RAY DIFFRACTIONf_chiral_restr0.071568
X-RAY DIFFRACTIONf_plane_restr0.005684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3508-2.39870.26391120.22272540X-RAY DIFFRACTION97
2.3987-2.45090.26261320.21542578X-RAY DIFFRACTION100
2.4509-2.50790.26441540.20632631X-RAY DIFFRACTION100
2.5079-2.57060.28081450.20692552X-RAY DIFFRACTION100
2.5706-2.64010.31791370.212602X-RAY DIFFRACTION100
2.6401-2.71780.3021530.21022558X-RAY DIFFRACTION100
2.7178-2.80550.27121740.19862598X-RAY DIFFRACTION100
2.8055-2.90580.27751380.1712598X-RAY DIFFRACTION100
2.9058-3.02210.19271320.17212594X-RAY DIFFRACTION100
3.0221-3.15960.26191280.18012601X-RAY DIFFRACTION100
3.1596-3.32620.22981410.19642611X-RAY DIFFRACTION100
3.3262-3.53450.25491360.18482585X-RAY DIFFRACTION100
3.5345-3.80730.21011670.17262573X-RAY DIFFRACTION100
3.8073-4.19030.20611200.16372592X-RAY DIFFRACTION100
4.1903-4.79620.15491490.1452583X-RAY DIFFRACTION100
4.7962-6.0410.22061380.17342577X-RAY DIFFRACTION99
6.041-49.6270.17091240.19252593X-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)
13.874-1.0265-0.50453.36760.46371.2530.0636-0.0287-0.3331-0.0293-0.04380.1581-0.0317-0.14060.01020.1819-0.01350.00130.15390.01820.152447.231119.744140.6525
23.6395-1.497-0.66353.20270.05791.63120.05050.06650.1909-0.043-0.0424-0.0904-0.0918-0.0209-0.01640.1968-0.0174-0.02920.15870.01980.165843.811942.117744.1661
33.64491.5313-0.12413.0646-0.94891.3944-0.0412-0.143-0.2627-0.0041-0.012-0.1945-0.05040.16160.06640.18660.03210.020.1602-0.01320.151850.7663-29.557547.0212
42.88790.9751-0.80843.4786-0.69572.4530.0501-0.05230.25-0.0709-0.0322-0.2562-0.08050.0586-0.03540.1560.03320.00520.1524-0.00140.186654.0624-7.385741.9676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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