[English] 日本語
Yorodumi
- PDB-2riu: Alternative models for two crystal structures of Candida albicans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2riu
TitleAlternative models for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase- alternate interpreation
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsISOMERASE / alternate model / Magnesium / Manganese / Metal-binding / Riboflavin biosynthesis
Function / homology
Function and homology information


3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / metal ion binding
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
RIBULOSE-5-PHOSPHATE / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsStenkamp, R.E. / Le Trong, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Alternative models for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase.
Authors: Le Trong, I. / Stenkamp, R.E.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans.
Authors: Echt, S. / Bauer, S. / Steinbacher, S. / Huber, R. / Bacher, A. / Fischer, M.
History
DepositionOct 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9152
Polymers22,6851
Non-polymers2301
Water2,720151
1
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules

A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8304
Polymers45,3702
Non-polymers4602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.597, 47.900, 40.200
Angle α, β, γ (deg.)90.000, 70.620, 90.000
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 22684.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: RIB3 / Plasmid: pnco-carib3-syn / Production host: Escherichia coli (E. coli) / Strain (production host): xl1 / References: UniProt: Q5A3V6
#2: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE / Ribulose 5-phosphate


Type: saccharideCarbohydrate / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.19 Å3/Da / Density % sol: 43.94 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.66→51.71 Å / Num. obs: 20361

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementResolution: 1.7→51.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.734 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1050 5.2 %RANDOM
Rwork0.185 ---
obs0.187 20361 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.836 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20.33 Å2
2--0.85 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 14 151 1686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221553
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.9982098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6324.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0661511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021153
X-RAY DIFFRACTIONr_nbd_refined0.2070.2792
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.227
X-RAY DIFFRACTIONr_mcbond_it0.4681.5996
X-RAY DIFFRACTIONr_mcangle_it0.76421558
X-RAY DIFFRACTIONr_scbond_it1.4483611
X-RAY DIFFRACTIONr_scangle_it2.3984.5540
LS refinement shellResolution: 1.7→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 72 -
Rwork0.23 1328 -
all-1400 -
obs--87.55 %

+
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