[English] 日本語
Yorodumi
- PDB-2ara: APO FORM OF ESCHERICHIA COLI REGULATORY PROTEIN ARAC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ara
TitleAPO FORM OF ESCHERICHIA COLI REGULATORY PROTEIN ARAC
ComponentsARAC
KeywordsTRANSCRIPTION REGULATION / JELLY-ROLL / CARBOHYDRATE BINDING / COILED-COIL
Function / homology
Function and homology information


arabinose catabolic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / identical protein binding / cytosol
Similarity search - Function
Regulatory protein AraC / Transcription regulator HTH-like / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. ...Regulatory protein AraC / Transcription regulator HTH-like / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Arabinose operon regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSoisson, S.M. / Wolberger, C.
CitationJournal: Science / Year: 1997
Title: Structural basis for ligand-regulated oligomerization of AraC.
Authors: Soisson, S.M. / MacDougall-Shackleton, B. / Schleif, R. / Wolberger, C.
History
DepositionOct 30, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ARAC


Theoretical massNumber of molelcules
Total (without water)17,4271
Polymers17,4271
Non-polymers00
Water0
1
A: ARAC

A: ARAC


Theoretical massNumber of molelcules
Total (without water)34,8542
Polymers34,8542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)57.370, 57.370, 83.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsCRYSTALLOGRAPHIC SYMMETRY GENERATES TWO POSSIBLE DIMER FORMS OF ARAC. THESE DIMER FORMS ARE DESCRIBED IN THE JRNL REFERENCE.

-
Components

#1: Protein ARAC / ARABINOSE OPERON REGULATORY PROTEIN


Mass: 17426.826 Da / Num. of mol.: 1 / Fragment: SUGAR-BINDING/DIMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARAC / Gene (production host): ARAC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9E0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: PROTEIN WAS CRYSTALLIZED BY HANGING-DROP VAPOR DIFFUSION FROM 20% PEG 4000, 0.1M TRIS-HCL, PH 9.0, 5 MM KCL, 0.2 M SODIUM ACETATE., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
20.1 MTris-HCl1reservoir
35 mM1reservoirKCl
40.2 Msodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.072
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: SPHERICAL RH COATED MIRROR
RadiationMonochromator: SAGITALLY FOCUSED SI(111) DOUBLE CRYSTAL MONOCHROMATOR
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 4676 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→2.82 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 3 / Rsym value: 0.293 / % possible all: 99
Reflection
*PLUS
Num. measured all: 51550

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ARC

2arc


Resolution: 2.8→7 Å / Rfactor Rfree error: 0.0185 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: SIMULATED-ANNEALING TORSION ANGLE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.337 329 10 %RANDOM
Rwork0.216 ---
obs0.216 3796 97.4 %-
Displacement parametersBiso mean: 31.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 0 0 1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.676.99
X-RAY DIFFRACTIONx_mcangle_it5.1110.22
X-RAY DIFFRACTIONx_scbond_it6.579.86
X-RAY DIFFRACTIONx_scangle_it11.8811.88
LS refinement shellResolution: 2.8→2.92 Å / Rfactor Rfree error: 0.085 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.541 43 10 %
Rwork0.335 409 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

+
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