[English] 日本語
Yorodumi
- PDB-8xod: ThDP-dependent HKA synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xod
TitleThDP-dependent HKA synthase
ComponentsBbmA-G484F complex with CBOA
KeywordsBIOSYNTHETIC PROTEIN / ThDP-dependent HKA synthase / mutant of BbmA
Function / homology: / ADENOSINE-5'-DIPHOSPHATE / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesBrevibacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsYu, J.H. / Liu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: ThDP-dependent HKA synthase
Authors: Yu, J.H. / Liu, T.
History
DepositionJan 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BbmA-G484F complex with CBOA
B: BbmA-G484F complex with CBOA
C: BbmA-G484F complex with CBOA
D: BbmA-G484F complex with CBOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,63815
Polymers249,9034
Non-polymers3,73511
Water1267
1
A: BbmA-G484F complex with CBOA
D: BbmA-G484F complex with CBOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8738
Polymers124,9522
Non-polymers1,9226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-67 kcal/mol
Surface area33730 Å2
MethodPISA
2
B: BbmA-G484F complex with CBOA
C: BbmA-G484F complex with CBOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7657
Polymers124,9522
Non-polymers1,8135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-77 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.935, 116.695, 201.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
BbmA-G484F complex with CBOA


Mass: 62475.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Non-polymers , 5 types, 18 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-A1LX0 / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(~{R})-cyclobutyl(oxidanyl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 509.431 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H27N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 24% polyethlene glycol 400, 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→24.94 Å / Num. obs: 59507 / % possible obs: 99.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 8.9
Reflection shellResolution: 2.75→2.83 Å / Rmerge(I) obs: 0.619 / Num. unique obs: 4562

-
Processing

Software
NameVersionClassification
PHENIX1.1.17.3360refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.75→24.94 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2864 --
Rwork0.203 --
obs-59507 99.8 %
Refinement stepCycle: LAST / Resolution: 2.75→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15846 0 233 7 16086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013716443
X-RAY DIFFRACTIONf_angle_d1.489122395
X-RAY DIFFRACTIONf_chiral_restr0.09352565
X-RAY DIFFRACTIONf_plane_restr0.00922861
X-RAY DIFFRACTIONf_dihedral_angle_d22.89035923

+
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