[English] 日本語
Yorodumi
- PDB-4xax: Crystal structure of Thermus thermophilus CarD in complex with th... -

+
Open data


ID or keywords:

Loading...

-
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 1Polymerase
KeywordsTranscription Regulator
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
CarD-like, C-terminal domain / : / CarD, C-terminal / CarD-like, 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 ...CarD-like, C-terminal domain / : / CarD, C-terminal / CarD-like, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein DNA-directed RNA polymerase subunit beta domain 1 / Polymerase / 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 / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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: 0

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

-
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

+
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