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- PDB-3tbi: Crystal structure of T4 gp33 bound to E. coli RNAP beta-flap domain -

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Basic information

Entry
Database: PDB / ID: 3tbi
TitleCrystal structure of T4 gp33 bound to E. coli RNAP beta-flap domain
Components
  • DNA-directed RNA polymerase subunit betaPolymerase
  • RNA polymerase-associated protein Gp33
KeywordsTRANSCRIPTION / transcription accessory protein
Function / homology
Function and homology information


late viral transcription / transcription regulator activator activity / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex ...late viral transcription / transcription regulator activator activity / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / response to antibiotic / DNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
Phage late-transcription coactivator-like / Late transcription coactivator / Phage late-transcription coactivator superfamily / Late transcription coactivator, myovirus / Phage late-transcription coactivator / Helix Hairpins - #1670 / RNA polymerase II, Rpb2 subunit, wall domain / Helix Hairpins / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain ...Phage late-transcription coactivator-like / Late transcription coactivator / Phage late-transcription coactivator superfamily / Late transcription coactivator, myovirus / Phage late-transcription coactivator / Helix Hairpins - #1670 / RNA polymerase II, Rpb2 subunit, wall domain / Helix Hairpins / 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 / Helix non-globular / 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 / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta / Late transcription coactivator
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsTwist, K.A.F. / Campbell, E.A. / Darst, S.A.
CitationJournal: To be Published
Title: Crystal structure of T4 gp33 bound to E. coli RNAP beta-flap domain
Authors: Twist, K.A.F. / Campbell, E.A. / Darst, S.A. / Geiduschek, E.P. / Hochschild, A. / Deighan, P.
History
DepositionAug 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase-associated protein Gp33
B: DNA-directed RNA polymerase subunit beta


Theoretical massNumber of molelcules
Total (without water)38,6482
Polymers38,6482
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-14 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.218, 112.250, 164.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein RNA polymerase-associated protein Gp33 / gp33 late promoter transcription accessory protein


Mass: 13276.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 33, gp33 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13338
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 25371.717 Da / Num. of mol.: 1 / Fragment: beta-flap domain (UNP residues 831-1057)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: b3987, groN, JW3950, nitB, rif, ron, rpoB, stl, stv, tabD
Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8V2, DNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M triethylamine N-oxide, 20% PEG2000 MME, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.9785 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→28.995 Å / Num. all: 10635 / Num. obs: 10551 / Redundancy: 3 % / Rsym value: 0.053

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3→28.995 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.889 / SU B: 20.43 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R: 1.363 / ESU R Free: 0.434
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29485 500 4.7 %RANDOM
Rwork0.25086 ---
obs0.25293 10051 98.93 %-
all-9980 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 112.814 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å2-0 Å20 Å2
2--5.16 Å2-0 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 3→28.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 0 0 2331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0222353
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6562.0043167
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9655297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20825.849106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02815451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1951514
X-RAY DIFFRACTIONr_chiral_restr0.0470.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3221.51482
X-RAY DIFFRACTIONr_mcbond_other0.0331.5607
X-RAY DIFFRACTIONr_mcangle_it0.60722387
X-RAY DIFFRACTIONr_scbond_it0.6893868
X-RAY DIFFRACTIONr_scangle_it1.2114.5777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 30 -
Rwork0.399 643 -
obs--95.19 %
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)
11.45991.65320.94782.76172.862910.11310.08330.02730.1063-0.09380.10520.0345-0.045-0.0238-0.18840.0576-0.02980.02890.0857-0.08830.1215-13.05519.56416.374
29.84721.16998.22710.7999-0.112410.34910.25130.5964-0.45710.1171-0.0911-0.41090.85791.1083-0.16020.4190.1493-0.19690.3697-0.30.656522.43917.70546.018
33.58233.62194.270910.14224.803210.4924-0.82220.88480.5347-1.82520.58570.8298-1.96750.49240.23640.501-0.079-0.06620.46680.04960.3091-16.78612.965-13.691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B830 - 941
2X-RAY DIFFRACTION1B1041 - 1057
3X-RAY DIFFRACTION2B942 - 1040
4X-RAY DIFFRACTION3A35 - 102

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