[English] 日本語
Yorodumi
- PDB-6xxg: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xxg
TitleStructure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans
Components1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / : / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsGierse, R.M. / Reddem, E. / Grooves, M.R.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research731.015.414 Netherlands
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Identification of a 1-deoxy-D-xylulose-5-phosphate synthase (DXS) mutant with improved crystallographic properties.
Authors: Gierse, R.M. / Reddem, E.R. / Alhayek, A. / Baitinger, D. / Hamid, Z. / Jakobi, H. / Laber, B. / Lange, G. / Hirsch, A.K.H. / Groves, M.R.
History
DepositionJan 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: 1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase
BBB: 1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,01015
Polymers126,7982
Non-polymers1,21313
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-171 kcal/mol
Surface area36550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.321, 87.367, 181.865
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxyxylulose-5-phosphate synthase / DXPS


Mass: 63398.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A loop of the native gene was deleted between amino acid 201 and 243. It was replaced with 7xG. more details in the related publication.,A loop of the native gene was deleted between amino ...Details: A loop of the native gene was deleted between amino acid 201 and 243. It was replaced with 7xG. more details in the related publication.,A loop of the native gene was deleted between amino acid 201 and 243. It was replaced with 7xG. more details in the related publication.
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Gene: dxs, DR_1475 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9RUB5, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M Tris, 20 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2017
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.099→47.549 Å / Num. obs: 67987 / % possible obs: 99.08 % / Redundancy: 2 % / CC1/2: 0.913 / Net I/σ(I): 5.87
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 6677 / CC1/2: 0.444 / % possible all: 99.48

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
XDSVERSION Mar 15, 2019 BUILT=20190315data scaling
MOLREPVers 11.7.02; 29.05.2019phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o1x

2o1x


Resolution: 2.099→47.549 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.166 / Average fsc free: 0.8887 / Average fsc work: 0.9025 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.236 3427 5.077 %
Rwork0.1908 64070 -
all0.193 --
obs-67497 98.976 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.023 Å2-0 Å2-0 Å2
2--0.007 Å20 Å2
3---0.016 Å2
Refinement stepCycle: LAST / Resolution: 2.099→47.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8274 0 63 481 8818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138539
X-RAY DIFFRACTIONr_bond_other_d0.0360.0178039
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.63311612
X-RAY DIFFRACTIONr_angle_other_deg2.3431.57518536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39651103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13921.227432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.664151353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2131565
X-RAY DIFFRACTIONr_chiral_restr0.0620.21105
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029735
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021788
X-RAY DIFFRACTIONr_nbd_refined0.1830.21744
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.27298
X-RAY DIFFRACTIONr_nbtor_refined0.1490.24079
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0640.23716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2478
X-RAY DIFFRACTIONr_metal_ion_refined0.2460.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.215
X-RAY DIFFRACTIONr_nbd_other0.210.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.26
X-RAY DIFFRACTIONr_mcbond_it1.6982.9354415
X-RAY DIFFRACTIONr_mcbond_other1.6972.9354414
X-RAY DIFFRACTIONr_mcangle_it2.694.3915517
X-RAY DIFFRACTIONr_mcangle_other2.694.3925518
X-RAY DIFFRACTIONr_scbond_it2.0933.2334124
X-RAY DIFFRACTIONr_scbond_other2.0893.234117
X-RAY DIFFRACTIONr_scangle_it3.4444.7416095
X-RAY DIFFRACTIONr_scangle_other3.4434.7426096
X-RAY DIFFRACTIONr_lrange_it5.2335.2229423
X-RAY DIFFRACTIONr_lrange_other5.19835.1029344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.099-2.1530.3012290.2694587X-RAY DIFFRACTION97.4504
2.153-2.2120.2762460.2514599X-RAY DIFFRACTION99.8146
2.212-2.2760.4532330.4464139X-RAY DIFFRACTION92.3142
2.276-2.3460.3042350.2334344X-RAY DIFFRACTION99.9127
2.346-2.4230.3122140.2264269X-RAY DIFFRACTION99.9331
2.423-2.5080.2662400.214032X-RAY DIFFRACTION99.9298
2.508-2.6030.2662190.2073950X-RAY DIFFRACTION99.9281
2.603-2.7090.2382050.1873802X-RAY DIFFRACTION99.9501
2.709-2.8290.2371950.1883659X-RAY DIFFRACTION99.9481
2.829-2.9670.2451900.1833509X-RAY DIFFRACTION99.8381
2.967-3.1270.2061560.173353X-RAY DIFFRACTION99.5743
3.127-3.3170.2181640.1763151X-RAY DIFFRACTION99.6393
3.317-3.5460.2311630.1772980X-RAY DIFFRACTION99.7145
3.546-3.8290.2311530.1652758X-RAY DIFFRACTION98.7784
3.829-4.1940.1851410.1392542X-RAY DIFFRACTION99.1134
4.194-4.6880.1611400.1352309X-RAY DIFFRACTION99.1498
4.688-5.410.2081090.1512076X-RAY DIFFRACTION99.5898
5.41-6.6210.253770.1761795X-RAY DIFFRACTION99.5215
6.621-9.3380.18720.1551402X-RAY DIFFRACTION98.9926
9.338-47.5490.174460.199814X-RAY DIFFRACTION97.0655

+
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