[English] 日本語
Yorodumi
- PDB-3lrj: Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lrj
TitleCrystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate ion.
Components3,4-Dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE / ENZYME-SULFATE COMPLEX / ALPHA+BETA BARREL / DRUG TARGET / antibacterial / Metal-binding / Riboflavin biosynthesis
Function / homology
Function and homology information


GTP cyclohydrolase II activity / 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
DHBP synthase / 3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsKumar, P. / Karthikeyan, S.
CitationJournal: Proteins / Year: 2010
Title: Potential anti-bacterial drug target: structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2.
Authors: Kumar, P. / Singh, M. / Gautam, R. / Karthikeyan, S.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3,4-Dihydroxy-2-butanone 4-phosphate synthase
B: 3,4-Dihydroxy-2-butanone 4-phosphate synthase
C: 3,4-Dihydroxy-2-butanone 4-phosphate synthase
D: 3,4-Dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,91810
Polymers93,3424
Non-polymers5766
Water1,02757
1
A: 3,4-Dihydroxy-2-butanone 4-phosphate synthase
B: 3,4-Dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9595
Polymers46,6712
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-24 kcal/mol
Surface area15490 Å2
MethodPISA
2
C: 3,4-Dihydroxy-2-butanone 4-phosphate synthase
D: 3,4-Dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9595
Polymers46,6712
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-22 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.370, 50.530, 76.200
Angle α, β, γ (deg.)75.92, 85.88, 76.19
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 9:33 or resseq 40:212 ) and (not element H) and (not element D)
211chain B and (resseq 9:33 or resseq 40:212 ) and (not element H) and (not element D)
311chain C and (resseq 9:33 or resseq 40:212 ) and (not element H) and (not element D)
411chain D and (resseq 9:33 or resseq 40:212 ) and (not element H) and (not element D)

-
Components

#1: Protein
3,4-Dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase


Mass: 23335.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ribB, STM3195 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P66032, 3,4-dihydroxy-2-butanone-4-phosphate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 8000, 100mM MES, 0.2M Ammonium sulphate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97869 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 16185 / Num. obs: 15424 / % possible obs: 88.73 % / Observed criterion σ(F): 1.98 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 41.55 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.064 / Net I/σ(I): 7.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2259 / Rsym value: 0.21 / % possible all: 88.8

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
CCP4model building
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G57

1g57


Resolution: 2.803→48.909 Å / SU ML: 0.34 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.98 / σ(I): 2 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 786 5.1 %throughout
Rwork0.2091 ---
all0.2123 16185 --
obs0.2123 15399 88.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.257 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 0.5935 Å2
Baniso -1Baniso -2Baniso -3
1--6.5613 Å2-22.7037 Å28.318 Å2
2--0.1698 Å25.0249 Å2
3---6.3915 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.803→48.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5907 0 30 57 5994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086009
X-RAY DIFFRACTIONf_angle_d1.0558145
X-RAY DIFFRACTIONf_dihedral_angle_d16.4882179
X-RAY DIFFRACTIONf_chiral_restr0.061964
X-RAY DIFFRACTIONf_plane_restr0.0041074
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1457X-RAY DIFFRACTIONPOSITIONAL
12B1457X-RAY DIFFRACTIONPOSITIONAL0.051
13C1472X-RAY DIFFRACTIONPOSITIONAL0.039
14D1457X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.803-2.97860.31941250.2603243588
2.9786-3.20860.30771400.247239489
3.2086-3.53140.33081420.2153245689
3.5314-4.04220.28911280.2062244589
4.0422-5.09180.25191270.172245889
5.0918-48.91610.20321240.1999242588

+
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