[English] 日本語
Yorodumi
- PDB-2htb: Crystal Structure of a putative mutarotase (YeaD) from Salmonella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2htb
TitleCrystal Structure of a putative mutarotase (YeaD) from Salmonella typhimurium in monoclinic form
ComponentsPutative enzyme related to aldose 1-epimerase
KeywordsISOMERASE / Salmonella typhimurium / carbohydrate / aldose 1-epimerase / mutarotase / YeaD / GalM / sugar phosphate
Function / homology
Function and homology information


glucose-6-phosphate 1-epimerase / glucose-6-phosphate 1-epimerase activity / carbohydrate binding / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Glucose-6-phosphate 1-epimerase / Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative glucose-6-phosphate 1-epimerase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChittori, S. / Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the putative mutarotase YeaD from Salmonella typhimurium: structural comparison with galactose mutarotases.
Authors: Chittori, S. / Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Putative enzyme related to aldose 1-epimerase
B: Putative enzyme related to aldose 1-epimerase
C: Putative enzyme related to aldose 1-epimerase
D: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)137,3754
Polymers137,3754
Non-polymers00
Water5,801322
1
A: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)34,3441
Polymers34,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)34,3441
Polymers34,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)34,3441
Polymers34,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative enzyme related to aldose 1-epimerase


Theoretical massNumber of molelcules
Total (without water)34,3441
Polymers34,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.553, 47.599, 138.086
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Putative enzyme related to aldose 1-epimerase


Mass: 34343.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: IFO12529 / Gene: yeaD / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
References: UniProt: Q8ZPV9, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15-25% PEG8K, 0.1M citrate pH 5.5, 0.2-0.5mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 13, 2005 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 50200 / % possible obs: 0.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.22 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4503 / % possible all: 0.919

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: monomer of orthorhombic form of stYeaD (PDB code 2HTA)

2hta


Resolution: 2.5→27.8 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.525 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23974 2480 5 %RANDOM
Rwork0.18877 ---
all0.19135 50310 --
obs0.19135 47276 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.472 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.02 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9112 0 0 322 9434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0219357
X-RAY DIFFRACTIONr_angle_refined_deg2.3141.93712794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.60251179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06724.269417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.629151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8961545
X-RAY DIFFRACTIONr_chiral_restr0.1570.21445
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027231
X-RAY DIFFRACTIONr_nbd_refined0.2380.24232
X-RAY DIFFRACTIONr_nbtor_refined0.3250.26246
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2532
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.28
X-RAY DIFFRACTIONr_mcbond_it1.7341.56046
X-RAY DIFFRACTIONr_mcangle_it2.17429540
X-RAY DIFFRACTIONr_scbond_it3.98633764
X-RAY DIFFRACTIONr_scangle_it5.5484.53254
LS refinement shellResolution: 2.499→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 153 -
Rwork0.319 3108 -
obs--91.01 %

+
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