[English] 日本語
Yorodumi
- PDB-3tbi: Crystal structure of T4 gp33 bound to E. coli RNAP beta-flap domain -

+
Open data


ID or keywords:

Loading...

-
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 beta
  • 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 / DNA-templated transcription initiation / transcription antitermination / cell motility / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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 / 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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more