[English] 日本語
Yorodumi
- PDB-5xgf: The fatty acid-responsive FadR repressor of Vibrio alginolyticus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xgf
TitleThe fatty acid-responsive FadR repressor of Vibrio alginolyticus
ComponentsFatty acid metabolism regulator protein
KeywordsTRANSCRIPTION / fatty acid-responsive FadR repressor / palmitoyl1-CoA ester binding / DNA binding
Function / homology
Function and homology information


fatty-acyl-CoA binding / regulation of fatty acid metabolic process / fatty acid metabolic process / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Fatty acid response transcription factor FadR / FadR, C-terminal domain / FadR C-terminal domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesVibrio alginolyticus E0666 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLin, Y. / Li, D.F. / Feng, Y.J.
CitationJournal: To Be Published
Title: Snapshort of Vibrio FadR-ligand complex structure reveals a new mechanism for bacterial fatty acid sensing
Authors: Feng, Y.J. / Lin, Y. / Li, D.F. / Zhang, H.M. / Gao, R.S. / Bi, L.J. / Wang, S.H.
History
DepositionApr 13, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 31, 2017ID: 5DV1
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4642
Polymers34,4051
Non-polymers591
Water2,000111
1
A: Fatty acid metabolism regulator protein
hetero molecules

A: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9284
Polymers68,8102
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3620 Å2
ΔGint-25 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.000, 76.000, 144.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Fatty acid metabolism regulator protein / GntR family transscriptional regulator


Mass: 34405.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus E0666 (bacteria) / Strain: E0666 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H0Y8X2*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.03 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200mM Calcium Acetate, 100mM Sodium Cacodylate pH 6.5, 7% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→18.474 Å / Num. obs: 18014 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 14
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.4 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E2X

1e2x


Resolution: 2.35→18.474 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.92
RfactorNum. reflection% reflection
Rfree0.2558 1800 10 %
Rwork0.2183 --
obs0.222 17995 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→18.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 1 111 2312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032247
X-RAY DIFFRACTIONf_angle_d0.6633037
X-RAY DIFFRACTIONf_dihedral_angle_d7.4051358
X-RAY DIFFRACTIONf_chiral_restr0.041331
X-RAY DIFFRACTIONf_plane_restr0.004393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.41340.31271280.26941161X-RAY DIFFRACTION95
2.4134-2.48430.27441380.24781237X-RAY DIFFRACTION99
2.4843-2.56430.2731390.24721241X-RAY DIFFRACTION100
2.5643-2.65570.31171370.24451241X-RAY DIFFRACTION100
2.6557-2.76170.24631380.23841240X-RAY DIFFRACTION100
2.7617-2.88690.23451380.23161245X-RAY DIFFRACTION100
2.8869-3.03850.2731400.23221260X-RAY DIFFRACTION100
3.0385-3.22790.28581380.2251241X-RAY DIFFRACTION100
3.2279-3.47560.22741400.22231256X-RAY DIFFRACTION99
3.4756-3.82260.2761370.20081242X-RAY DIFFRACTION98
3.8226-4.36930.21441420.19881268X-RAY DIFFRACTION99
4.3693-5.48090.241350.19891225X-RAY DIFFRACTION94
5.4809-18.47450.26861500.21521338X-RAY DIFFRACTION96
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)
10.1207-0.2520.57750.7769-1.49783.0798-0.84980.49151.91110.2447-0.1376-0.6404-2.05281.68980.90312.3039-0.7648-0.65261.21530.18991.89480.264715.76826.4559
24.2044-1.65821.23475.4938-2.36841.1501-0.7381-0.58631.6460.85530.0443-0.1689-1.90440.27990.12920.8677-0.158-0.21170.454-0.03120.982-7.79946.8524.7404
33.68-1.00050.43412.5658-1.34854.9337-0.0652-0.4150.0650.22460.119-0.2440.07040.7097-0.07570.19270.0516-0.05540.4214-0.0150.2401-2.9021-19.64412.6713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 278 )

+
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