[English] 日本語
Yorodumi
- PDB-1ui6: Crystal structure of gamma-butyrolactone receptor (ArpA-like protein) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ui6
TitleCrystal structure of gamma-butyrolactone receptor (ArpA-like protein)
ComponentsA-factor receptor homolog
KeywordsANTIBIOTIC / helix-turn-helix / alpha-helix bundle
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily ...: / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNatsume, R. / Senda, T. / Horinouchi, S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of a gamma-butyrolactone autoregulator receptor protein in Streptomyces coelicolor A3(2)
Authors: Natsume, R. / Ohnishi, Y. / Senda, T. / Horinouchi, S.
History
DepositionJul 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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: A-factor receptor homolog
B: A-factor receptor homolog


Theoretical massNumber of molelcules
Total (without water)47,4392
Polymers47,4392
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-11 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.792, 69.562, 148.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a dimer that is contained in the asymmetric unit.

-
Components

#1: Protein A-factor receptor homolog / CprB / bacterial autoregulator receptor protein / gamma-butyrolactone receptor


Mass: 23719.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Production host: Escherichia coli (E. coli) / References: UniProt: O66122
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.27 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6000, lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 18, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 31849 / Num. obs: 31849 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3591 / Rsym value: 0.205 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UI5

1ui5


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.869 / SU B: 13.834 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.782 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28401 751 5.1 %RANDOM
Rwork0.22493 ---
all0.22787 15231 --
obs0.22787 13950 91.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2---0.68 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 0 57 3082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213079
X-RAY DIFFRACTIONr_bond_other_d0.0010.022970
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9564171
X-RAY DIFFRACTIONr_angle_other_deg0.81836795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2643382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0915551
X-RAY DIFFRACTIONr_chiral_restr0.0850.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023413
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02685
X-RAY DIFFRACTIONr_nbd_refined0.260.3794
X-RAY DIFFRACTIONr_nbd_other0.2190.32848
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5106
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.358
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2970.512
X-RAY DIFFRACTIONr_mcbond_it0.8741.51921
X-RAY DIFFRACTIONr_mcangle_it1.66823085
X-RAY DIFFRACTIONr_scbond_it2.69431158
X-RAY DIFFRACTIONr_scangle_it4.7054.51086
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 63
Rwork0.214 993
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)
11.4497-1.19952.10363.02711.52063.92950.156-0.0224-0.274-0.1825-0.0612-0.03270.3488-0.2806-0.09480.1078-0.02410.04740.06720.00010.12356.21766.806-8.409
20.4153-0.2445-0.49441.4544-0.2392.63110.0080.01-0.01230.14480.00040.0825-0.0186-0.0149-0.00850.05860.0205-0.00860.1156-0.01790.095260.34387.47215.191
34.53610.64481.33933.13040.98223.02980.0121-0.15680.0807-0.3695-0.04660.17930.00790.01980.03460.17-0.0178-0.0390.1047-0.04070.072350.96749.62922.398
41.28920.28790.39392.38661.00172.0333-0.12960.01620.02-0.18080.10650.096-0.07960.01920.02310.1193-0.0023-0.05810.08340.05840.067648.04679.25731.019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 534 - 53
2X-RAY DIFFRACTION2AA75 - 21275 - 212
3X-RAY DIFFRACTION3BB6 - 536 - 53
4X-RAY DIFFRACTION4BB75 - 21275 - 212

+
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://pdbjlvh1.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