[English] 日本語
Yorodumi
- PDB-1ym5: Crystal structure of YHI9, the yeast member of the phenazine bios... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ym5
TitleCrystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.
ComponentsHypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region
KeywordsOXIDOREDUCTASE / PhzF enzyme superfamily / double hot-dog / Structural Genomics / Paris-Sud Yeast Structural Genomics / YSG
Function / homology
Function and homology information


Isomerases; Racemases and epimerases / biosynthetic process / endoplasmic reticulum unfolded protein response / isomerase activity / chromatin / cytoplasm
Similarity search - Function
Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized isomerase YHI9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.05 Å
AuthorsLiger, D. / Quevillon-Cheruel, S. / Sorel, I. / Bremang, M. / Blondeau, K. / Aboulfath, I. / Janin, J. / Van Tilbeurgh, H. / Leulliot, N. / Paris-Sud Yeast Structural Genomics (YSG)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily
Authors: Liger, D. / Quevillon-Cheruel, S. / Sorel, I. / Bremang, M. / Blondeau, K. / Aboulfath, I. / Janin, J. / van Tilbeurgh, H. / Leulliot, N.
History
DepositionJan 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region


Theoretical massNumber of molelcules
Total (without water)33,4271
Polymers33,4271
Non-polymers00
Water2,774154
1
A: Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region

A: Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region


Theoretical massNumber of molelcules
Total (without water)66,8542
Polymers66,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)81.188, 81.188, 98.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region / YHI9


Mass: 33427.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pet9 / Production host: Escherichia coli (E. coli) / References: UniProt: P38765
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 24% PEG 4000, 0.1M sodium acetate pH5, 0.2M ammonium acetate, 30% glycerol, 10mM DDT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 2003
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.04→62.5 Å / Num. all: 21203 / Num. obs: 21044 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.043→2.096 Å / % possible all: 92.69

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.067 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0.4 / ESU R: 0.193 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25112 1081 5.1 %RANDOM
Rwork0.18763 ---
all0.1908 21044 --
obs0.1908 19923 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.236 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2--1.13 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 0 154 2446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222343
X-RAY DIFFRACTIONr_bond_other_d0.0010.022124
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9643177
X-RAY DIFFRACTIONr_angle_other_deg0.84634979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74525.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10415408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.387156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
X-RAY DIFFRACTIONr_nbd_refined0.2070.2470
X-RAY DIFFRACTIONr_nbd_other0.1890.22145
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21138
X-RAY DIFFRACTIONr_nbtor_other0.0920.21412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4241.51873
X-RAY DIFFRACTIONr_mcbond_other0.2361.5590
X-RAY DIFFRACTIONr_mcangle_it1.66422384
X-RAY DIFFRACTIONr_scbond_it2.39931017
X-RAY DIFFRACTIONr_scangle_it3.3084.5793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.043→2.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 80 -
Rwork0.261 1340 -
obs--92.69 %

+
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://pdbjlvh1.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