[English] 日本語
Yorodumi
- PDB-5ckt: Crystal Structure of KorA, a plasmid-encoded, global transcriptio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ckt
TitleCrystal Structure of KorA, a plasmid-encoded, global transcription regulator
Components(TrfB transcriptional repressor protein) x 2
KeywordsTRANSCRIPTION / Helix-turn-helix
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #2690 / TrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / : / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / TrfB transcriptional repressor protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
Model detailsapo form
AuthorsWhite, S.A. / Hyde, E.I. / Lovering, A.L.
Citation
Journal: Nucleic Acids Res. / Year: 2016
Title: Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator.
Authors: Rajasekar, K.V. / Lovering, A.L. / Dancea, F. / Scott, D.J. / Harris, S.A. / Bingle, L.E. / Roessle, M. / Thomas, C.M. / Hyde, E.I. / White, S.A.
#1: Journal: Mol. Microbiol. / Year: 2008
Title: A single aromatic residue in transcriptional repressor protein KorA is critical for cooperativity with its co-regulator KorB.
Authors: Bingle, L.E. / Rajasekar, K.V. / Muntaha, S.t. / Nadella, V. / Hyde, E.I. / Thomas, C.M.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TrfB transcriptional repressor protein
B: TrfB transcriptional repressor protein
C: TrfB transcriptional repressor protein
D: TrfB transcriptional repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5556
Polymers44,4374
Non-polymers1182
Water3,891216
1
A: TrfB transcriptional repressor protein
D: TrfB transcriptional repressor protein


Theoretical massNumber of molelcules
Total (without water)22,3612
Polymers22,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-18 kcal/mol
Surface area11910 Å2
MethodPISA
2
B: TrfB transcriptional repressor protein
C: TrfB transcriptional repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1934
Polymers22,0752
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-17 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.580, 49.690, 52.330
Angle α, β, γ (deg.)98.090, 93.870, 106.010
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein TrfB transcriptional repressor protein / Regulatory protein KorA


Mass: 11037.534 Da / Num. of mol.: 3 / Fragment: KorA
Source method: isolated from a genetically manipulated source
Details: IncP-1 plasmid RK2 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trfB, korA / Plasmid: pET28a / Details (production host): derivative pGBT340 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03052
#2: Protein TrfB transcriptional repressor protein / Regulatory protein KorA


Mass: 11323.908 Da / Num. of mol.: 1 / Fragment: KorA
Source method: isolated from a genetically manipulated source
Details: IncP-1 plasmid RK2 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trfB, korA / Plasmid: pET28a / Details (production host): derivative pGBT340 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03052
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG 4000, sodium acetate, ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→27.17 Å / Num. obs: 26649 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rsym value: 0.031 / Net I/σ(I): 26.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.6 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
SOLVEphasing
RefinementResolution: 2→27.17 Å / FOM work R set: 0.8268 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 2704 5.11 %Random selection
Rwork0.1958 50230 --
obs0.1972 52934 96.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.3 Å2 / Biso mean: 55.86 Å2 / Biso min: 18.84 Å2
Refinement stepCycle: final / Resolution: 2→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 8 216 3298
Biso mean--41.84 48.25 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043165
X-RAY DIFFRACTIONf_angle_d0.8124277
X-RAY DIFFRACTIONf_chiral_restr0.043476
X-RAY DIFFRACTIONf_plane_restr0.003559
X-RAY DIFFRACTIONf_dihedral_angle_d15.5421192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9979-2.03420.30651230.29882466258990
2.0342-2.07330.32911730.28262603277697
2.0733-2.11570.26571240.26842669279395
2.1157-2.16160.31881540.26142666282096
2.1616-2.21190.27971480.24692531267997
2.2119-2.26720.2791330.23292721285496
2.2672-2.32850.21881460.22952670281697
2.3285-2.3970.22851140.20642665277996
2.397-2.47430.22551550.20432653280897
2.4743-2.56270.26511180.20722634275297
2.5627-2.66520.27191330.21442704283796
2.6652-2.78640.21841400.21022667280798
2.7864-2.93320.26271220.21792690281297
2.9332-3.11680.26221630.20632671283497
3.1168-3.35710.25061190.21712648276797
3.3571-3.69440.20121420.18752675281797
3.6944-4.22760.19181630.16042664282797
4.2276-5.32120.18791850.16172640282597
5.3212-29.34670.18861490.17132593274295
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)
12.66731.0445-0.37866.9347-0.26824.8382-0.0487-1.05220.08380.61930.1923-0.574-0.22450.2333-0.21450.34380.0931-0.02150.6763-0.08560.23317.0833.62636.2275
24.902-0.7823-0.05723.809-2.07115.7199-0.08320.4593-0.3182-0.6135-0.20550.03150.22230.41930.21440.29270.0083-0.00390.2423-0.04210.1617-1.3544-0.3272-18.1772
35.4045-1.36612.99056.8235-4.98058.4992-0.0470.2180.7910.41830.04030.2905-0.5776-0.0649-0.01530.5739-0.0602-0.01790.24090.07930.4728.1496-25.2207-28.6619
40.34970.65480.28553.6294-1.81083.92540.0092-0.6243-1.2777-0.16830.27720.1620.45750.0109-0.16530.34470.04480.00390.43030.31230.8203-4.002-19.0641-1.0101
51.98880.28760.16864.8916-0.1974.07910.1883-0.5922-0.40980.5411-0.12270.76330.5188-0.2268-0.06230.36310.03350.13250.52250.19930.630122.7258-10.25222.0235
67.0605-2.00631.64673.7206-0.83037.86880.66870.66420.5142-0.58790.06330.3349-0.0491-0.7579-0.60230.43210.01790.00430.51720.19370.871523.6452-6.8543-23.0728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq :65)A1 - 65
2X-RAY DIFFRACTION2(chain B and resseq :65)B1 - 65
3X-RAY DIFFRACTION3(chain C and resseq :65)C1 - 65
4X-RAY DIFFRACTION4(chain D and resseq :65)D3 - 65
5X-RAY DIFFRACTION5((chain A or chain D) and resseq 66:)A0
6X-RAY DIFFRACTION6((chain B or chain C) and resseq 66:)B0

+
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