[English] 日本語
Yorodumi
- PDB-8xix: KeDt3e within Co -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xix
TitleKeDt3e within Co
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / D-tagatose 3-epimerase
Function / homology: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / isomerase activity / D-tagatose 3-epimerase
Function and homology information
Biological speciesKroppenstedtia eburnea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsGuo, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Production of D-psicose
Authors: Guo, D.
History
DepositionDec 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-tagatose 3-epimerase


Theoretical massNumber of molelcules
Total (without water)33,0321
Polymers33,0321
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.310, 119.310, 47.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein D-tagatose 3-epimerase


Mass: 33031.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kroppenstedtia eburnea (bacteria) / Gene: SAMN05421790_10663 / Production host: Kroppenstedtia eburnea (bacteria) / References: UniProt: A0A1N7MFN7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop
Details: 2% v/v 1,4-dioxane 0.1 M Tris pH 8.0 15% w/v Polyethlene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Oct 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.16→44.78 Å / Num. obs: 18116 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 16.7
Reflection shellResolution: 2.36→2.45 Å / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1564

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VNK

3vnk


Resolution: 2.16→44.47 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.225 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25477 977 5.1 %RANDOM
Rwork0.20299 ---
obs0.20558 18116 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.248 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.16→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 0 72 2391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132369
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162256
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.6413201
X-RAY DIFFRACTIONr_angle_other_deg1.1611.5865193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30522.652132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78815423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6791515
X-RAY DIFFRACTIONr_chiral_restr0.0520.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6342.4531151
X-RAY DIFFRACTIONr_mcbond_other0.6342.4521149
X-RAY DIFFRACTIONr_mcangle_it1.0453.6761436
X-RAY DIFFRACTIONr_mcangle_other1.0453.6761436
X-RAY DIFFRACTIONr_scbond_it0.8052.5711217
X-RAY DIFFRACTIONr_scbond_other0.8052.5721218
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3613.8121765
X-RAY DIFFRACTIONr_long_range_B_refined2.59128.3712628
X-RAY DIFFRACTIONr_long_range_B_other2.47528.2322615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 71 -
Rwork0.263 1306 -
obs--98.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0685-1.10771.94891.1842-1.01631.4631-0.2844-0.11270.20310.25710.0989-0.1161-0.02540.06220.18550.22760.13770.01640.11150.020.025239.799911.732715.6196
23.08421.0883-0.88840.8425-0.4390.8869-0.0562-0.23390.06140.07880.02260.0234-0.05190.05470.03360.06010.0224-0.02620.04330.00310.067149.12969.641613.9035
30.77440.0454-0.1192.2235-0.63020.71740.04550.11610.06550.1108-0.0483-0.1243-0.04710.05960.00280.04180.00650.00490.0476-0.00230.059351.537819.7768-0.2671
41.5297-0.2993-0.01720.6706-0.17220.06560.02050.2052-0.0313-0.0058-0.0320.00590.006-0.00950.01150.05140.0221-0.0060.0955-0.0310.01737.613816.9105-5.3137
51.3725-0.69170.73680.5733-0.56190.56830.10950.0289-0.3302-0.0051-0.00980.09370.04640.007-0.09970.10760.0004-0.02120.0379-0.05360.162927.51094.1428-0.5328
61.4524-2.1344-0.61744.468-1.60825.04470.005-0.03850.25970.0733-0.0312-0.4285-0.17420.15920.02620.07470.0425-0.04470.0436-0.04650.12231.970225.445713.8285
74.91764.19535.65135.85046.12658.4474-0.1706-0.20710.04040.40150.03030.23040.2563-0.25920.14030.15550.03670.03760.05260.03040.034426.79968.22415.8934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 61
2X-RAY DIFFRACTION2A62 - 92
3X-RAY DIFFRACTION3A93 - 133
4X-RAY DIFFRACTION4A134 - 258
5X-RAY DIFFRACTION5A259 - 277
6X-RAY DIFFRACTION6A278 - 302
7X-RAY DIFFRACTION7A303 - 322

+
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