[English] 日本語
Yorodumi
- PDB-8vxk: Crystal Structure of the Apo Bacillus subtilis GabR C-terminal Ef... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vxk
TitleCrystal Structure of the Apo Bacillus subtilis GabR C-terminal Effector-binding and Oligomerization Domain
ComponentsHTH-type transcriptional regulatory protein GabR
KeywordsTRANSCRIPTION / MocR / GabR / PLP / Transcription Regulator
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
: / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / HTH-type transcriptional regulatory protein GabR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKaley, N.E. / Liu, D.
Funding support1items
OrganizationGrant numberCountry
Other government1R15GM113229-01
CitationJournal: Protein Sci. / Year: 2025
Title: Bioisosteric replacement of pyridoxal-5'-phosphate to pyridoxal-5'-tetrazole targeting Bacillus subtilis GabR.
Authors: Kaley, N.E. / Liveris, Z.J. / Moore, M. / Reidl, C.T. / Wawrzak, Z. / Becker, D.P. / Liu, D.
History
DepositionFeb 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HTH-type transcriptional regulatory protein GabR
B: HTH-type transcriptional regulatory protein GabR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5003
Polymers88,4052
Non-polymers951
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-28 kcal/mol
Surface area29190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.782, 118.782, 75.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein HTH-type transcriptional regulatory protein GabR


Mass: 44202.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: gabR, ycnF, BSU03890 / Plasmid: pETite C-His / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P94426
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 6% PEG 6000, 100mM HEPES pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12718 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12718 Å / Relative weight: 1
ReflectionResolution: 1.85→19.97 Å / Num. obs: 84313 / % possible obs: 94.77 % / Redundancy: 7.1 % / Biso Wilson estimate: 31.58 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 33025 / CC1/2: 0.397 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.81 Å / Cross valid method: FREE R-VALUE / σ(F): 17.35 / Phase error: 24.34 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2274 4118 4.88 %
Rwork0.1955 --
obs0.2078 84312 94.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 5 106 5883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115896
X-RAY DIFFRACTIONf_angle_d1.1777951
X-RAY DIFFRACTIONf_dihedral_angle_d6.53796
X-RAY DIFFRACTIONf_chiral_restr0.063875
X-RAY DIFFRACTIONf_plane_restr0.011019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.31632020.30394257X-RAY DIFFRACTION100
1.88-1.920.31391510.30912991X-RAY DIFFRACTION68
1.92-1.960.30772240.29074184X-RAY DIFFRACTION95
1.96-20.30492300.27474210X-RAY DIFFRACTION95
2-2.040.2862090.26454220X-RAY DIFFRACTION95
2.04-2.090.2681730.26443317X-RAY DIFFRACTION75
2.09-2.140.31651980.25524230X-RAY DIFFRACTION96
2.14-2.20.28512370.25164212X-RAY DIFFRACTION95
2.2-2.260.20991550.25742833X-RAY DIFFRACTION64
2.26-2.330.24852250.23874207X-RAY DIFFRACTION95
2.33-2.420.26161980.25244250X-RAY DIFFRACTION96
2.42-2.510.26482220.24174246X-RAY DIFFRACTION95
2.51-2.630.24462040.2414238X-RAY DIFFRACTION95
2.63-2.760.19652250.23433892X-RAY DIFFRACTION88
2.77-2.940.26792260.22434242X-RAY DIFFRACTION95
2.94-3.160.22852010.21884238X-RAY DIFFRACTION95
3.16-3.480.22042030.19554038X-RAY DIFFRACTION90
3.48-3.980.24851860.18143808X-RAY DIFFRACTION85
3.98-50.20252210.14894238X-RAY DIFFRACTION94
5-19.810.20452260.1634346X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 23.1401 Å / Origin y: -58.815 Å / Origin z: -19.7897 Å
111213212223313233
T0.1766 Å20.0013 Å2-0.0066 Å2-0.2058 Å20.01 Å2--0.0912 Å2
L0.2773 °20.0336 °2-0.0764 °2-0.1469 °20.1332 °2--0.4342 °2
S0.0432 Å °-0.0021 Å °0.0076 Å °0.0063 Å °-0.0546 Å °0.0029 Å °0.0064 Å °-0.0257 Å °-0.0005 Å °
Refinement TLS groupSelection details: all

+
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