[English] 日本語
Yorodumi
- PDB-6nwo: Structures of the transcriptional regulator BgaR, a lactose sensor. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nwo
TitleStructures of the transcriptional regulator BgaR, a lactose sensor.
ComponentsTranscriptional regulator BgaR
KeywordsTRANSCRIPTION / lactose transcriptional regulator / lactose sensor / SAD phasing
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
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
Similarity search - Domain/homology
beta-lactose / Probable transcriptional regulator
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsPeat, T.S. / Newman, J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structures of the transcriptional regulator BgaR, a lactose sensor.
Authors: Newman, J. / Caron, K. / Nebl, T. / Peat, T.S.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator BgaR
D: Transcriptional regulator BgaR
B: Transcriptional regulator BgaR
C: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4637
Polymers84,9934
Non-polymers4703
Water2,666148
1
A: Transcriptional regulator BgaR
D: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8393
Polymers42,4962
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-10 kcal/mol
Surface area15280 Å2
MethodPISA
2
B: Transcriptional regulator BgaR
C: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6244
Polymers42,4962
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-20 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.429, 40.482, 261.721
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22B
13A
23C
14D
24B
15D
25C
16B
26C

NCS domain segments:

Component-ID: 0 / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA10 - 16010 - 160
21LYSLYSDB10 - 16010 - 160
12GLUGLUAA11 - 16011 - 160
22GLUGLUBC11 - 16011 - 160
13LYSLYSAA10 - 16010 - 160
23LYSLYSCD10 - 16010 - 160
14GLUGLUDB11 - 16011 - 160
24GLUGLUBC11 - 16011 - 160
15ILEILEDB3 - 1603 - 160
25ILEILECD3 - 1603 - 160
16GLUGLUBC11 - 16011 - 160
26GLUGLUCD11 - 16011 - 160

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Transcriptional regulator BgaR


Mass: 21248.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Strain: 13 / Type A / Gene: CPE0770 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XMB9
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 5 mg/mL protein; 21.7% PEG 3350, 222mM MgCl2, 100mM bis-tris pH 5.7. Sitting drops were set up in 200 nL plus 200 nL volumes at 20C

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953723 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953723 Å / Relative weight: 1
ReflectionResolution: 2.11→43.62 Å / Num. obs: 41261 / % possible obs: 98.7 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.043 / Net I/σ(I): 9.4
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3104 / CC1/2: 0.744 / Rpim(I) all: 0.29 / % possible all: 91.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6nwh

6nwh


Resolution: 2.11→43.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.215 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 2066 5 %RANDOM
Rwork0.19376 ---
obs0.19559 39182 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.041 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å2-0.21 Å2
2--2.97 Å20 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 2.11→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5036 0 30 148 5214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135253
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174707
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.6427138
X-RAY DIFFRACTIONr_angle_other_deg1.3341.57510999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4825.31258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25315896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.453158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
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_it3.2164.0312544
X-RAY DIFFRACTIONr_mcbond_other3.214.0292543
X-RAY DIFFRACTIONr_mcangle_it4.5326.0283187
X-RAY DIFFRACTIONr_mcangle_other4.5326.0313188
X-RAY DIFFRACTIONr_scbond_it4.3564.572709
X-RAY DIFFRACTIONr_scbond_other4.3564.5712710
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7046.663952
X-RAY DIFFRACTIONr_long_range_B_refined9.17676.90521313
X-RAY DIFFRACTIONr_long_range_B_other9.17576.93521250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A48900.08
12D48900.08
21A48610.09
22B48610.09
31A48630.1
32C48630.1
41D48090.08
42B48090.08
51D50260.09
52C50260.09
61B48660.08
62C48660.08
LS refinement shellResolution: 2.113→2.168 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 131 -
Rwork0.26 2652 -
obs--91.31 %

+
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