[English] 日本語
Yorodumi
- PDB-6nx3: Structures of the transcriptional regulator BgaR, a lactose sensor. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nx3
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
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. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / 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. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / 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
beta-lactose / Probable transcriptional regulator
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 7, 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 / Data collection ...Atomic model / 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_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.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
B: Transcriptional regulator BgaR
C: Transcriptional regulator BgaR
D: Transcriptional regulator BgaR
E: Transcriptional regulator BgaR
F: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,54312
Polymers127,4896
Non-polymers2,0546
Water8,989499
1
A: Transcriptional regulator BgaR
D: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1814
Polymers42,4962
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-5 kcal/mol
Surface area14970 Å2
MethodPISA
2
B: Transcriptional regulator BgaR
hetero molecules

F: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1814
Polymers42,4962
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area2970 Å2
ΔGint-5 kcal/mol
Surface area14950 Å2
MethodPISA
3
C: Transcriptional regulator BgaR
E: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1814
Polymers42,4962
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-6 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.150, 46.317, 118.903
Angle α, β, γ (deg.)90.00, 100.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPROAA4 - 1614 - 161
21LEULEUPROPROBB4 - 1614 - 161
12LEULEUPROPROAA4 - 1614 - 161
22LEULEUPROPROCC4 - 1614 - 161
13LEULEULYSLYSAA4 - 1604 - 160
23LEULEULYSLYSDD4 - 1604 - 160
14LEULEULYSLYSAA4 - 1604 - 160
24LEULEULYSLYSEE4 - 1604 - 160
15LEULEULYSLYSAA4 - 1604 - 160
25LEULEULYSLYSFF4 - 1604 - 160
16LEULEUPROPROBB4 - 1614 - 161
26LEULEUPROPROCC4 - 1614 - 161
17LEULEULYSLYSBB4 - 1604 - 160
27LEULEULYSLYSDD4 - 1604 - 160
18LEULEULYSLYSBB4 - 1604 - 160
28LEULEULYSLYSEE4 - 1604 - 160
19LEULEULYSLYSBB4 - 1604 - 160
29LEULEULYSLYSFF4 - 1604 - 160
110LEULEULYSLYSCC4 - 1604 - 160
210LEULEULYSLYSDD4 - 1604 - 160
111LEULEULYSLYSCC4 - 1604 - 160
211LEULEULYSLYSEE4 - 1604 - 160
112LEULEULYSLYSCC4 - 1604 - 160
212LEULEULYSLYSFF4 - 1604 - 160
113ILEILEPROPRODD3 - 1613 - 161
213ILEILEPROPROEE3 - 1613 - 161
114ILEILEPROPRODD3 - 1613 - 161
214ILEILEPROPROFF3 - 1613 - 161
115ILEILEPROPROEE3 - 1613 - 161
215ILEILEPROPROFF3 - 1613 - 161

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Transcriptional regulator BgaR


Mass: 21248.188 Da / Num. of mol.: 6
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.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5 mg/mL protein; 20% PEG 3350, 200 mM MgCl2. Sitting drops were 200 nL plus 200 nL at 20C- no buffer was used in this crystallisation cocktail.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.45865 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45865 Å / Relative weight: 1
ReflectionResolution: 1.87→48.25 Å / Num. obs: 87904 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Net I/σ(I): 9.4
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4400 / CC1/2: 0.922 / Rpim(I) all: 0.352 / % possible all: 97.2

-
Processing

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

6nwh


Resolution: 1.87→46.86 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.817 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25374 4408 5 %RANDOM
Rwork0.22449 ---
obs0.22595 83468 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å21.62 Å2
2---1.03 Å2-0 Å2
3----1.66 Å2
Refinement stepCycle: 1 / Resolution: 1.87→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7683 0 138 499 8320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138231
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177378
X-RAY DIFFRACTIONr_angle_refined_deg1.471.66111213
X-RAY DIFFRACTIONr_angle_other_deg1.3641.59217284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26825.303396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.216151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.391512
X-RAY DIFFRACTIONr_chiral_restr0.0780.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021629
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_it2.3492.7543918
X-RAY DIFFRACTIONr_mcbond_other2.3492.7533917
X-RAY DIFFRACTIONr_mcangle_it3.3754.114929
X-RAY DIFFRACTIONr_mcangle_other3.3744.1124930
X-RAY DIFFRACTIONr_scbond_it3.4963.2224313
X-RAY DIFFRACTIONr_scbond_other3.4963.2224313
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4244.6696285
X-RAY DIFFRACTIONr_long_range_B_refined7.55253.07333897
X-RAY DIFFRACTIONr_long_range_B_other7.54152.98933564
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)
11A52620.05
12B52620.05
21A52670.04
22C52670.04
31A52120.07
32D52120.07
41A51970.07
42E51970.07
51A52130.07
52F52130.07
61B52880.04
62C52880.04
71B51770.07
72D51770.07
81B51730.07
82E51730.07
91B51810.07
92F51810.07
101C52540.06
102D52540.06
111C52480.06
112E52480.06
121C52660.06
122F52660.06
131D53700.03
132E53700.03
141D53810.03
142F53810.03
151E52830.03
152F52830.03
LS refinement shellResolution: 1.871→1.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 315 -
Rwork0.34 6101 -
obs--98.37 %

+
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