[English] 日本語
Yorodumi
- PDB-7dz3: Crystal structures of D-allulose 3-epimerase with D-fructose from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dz3
TitleCrystal structures of D-allulose 3-epimerase with D-fructose from Sinorhizobium fredii
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / D-allulose / rare sugar / Sinorhizobium fredii / D-allulose 3-epimerase
Function / homologyracemase and epimerase activity, acting on carbohydrates and derivatives / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / manganese ion binding / D-fructose / D-tagatose 3-epimerase
Function and homology information
Biological speciesSinorhizobium fredii CCBAU 83666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZhu, Z.L. / Miyakawa, T. / Tanokura, M. / Lu, F.P. / Qin, H.-M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening
Authors: Li, C. / Gao, X. / Qi, H. / Zhang, W. / Li, L. / Wei, C. / Wei, M. / Sun, X. / Wang, S. / Wang, L. / Ji, Y. / Mao, S. / Zhu, Z. / Tanokura, M. / Lu, F. / Qin, H.M.
History
DepositionJan 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-tagatose 3-epimerase
B: D-tagatose 3-epimerase
C: D-tagatose 3-epimerase
D: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,80410
Polymers125,3464
Non-polymers4586
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-48 kcal/mol
Surface area36830 Å2
Unit cell
Length a, b, c (Å)87.437, 120.648, 134.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
D-tagatose 3-epimerase


Mass: 31336.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium fredii CCBAU 83666 (bacteria)
Gene: SF83666_b55120 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: A0A249Q1V1, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-FUD / D-fructose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG 3,350

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→48.78 Å / Num. obs: 116087 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.54 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.046 / Rrim(I) all: 0.123 / Net I/σ(I): 10.3
Reflection shellResolution: 1.88→1.91 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5634 / CC1/2: 0.716 / Rpim(I) all: 0.481

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZFS

5zfs


Resolution: 1.88→44.92 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2184 5834 5.03 %
Rwork0.182 110131 -
obs0.1838 115965 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.32 Å2
Refinement stepCycle: LAST / Resolution: 1.88→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8772 0 4 375 9151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01088966
X-RAY DIFFRACTIONf_angle_d1.115112160
X-RAY DIFFRACTIONf_chiral_restr0.05561320
X-RAY DIFFRACTIONf_plane_restr0.00721596
X-RAY DIFFRACTIONf_dihedral_angle_d9.51871232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.32762010.2823585X-RAY DIFFRACTION98.13
1.9-1.920.30631880.25593589X-RAY DIFFRACTION98.46
1.92-1.940.29622020.23853594X-RAY DIFFRACTION98.34
1.94-1.970.27861960.22743598X-RAY DIFFRACTION98.47
1.97-1.990.28161760.23013651X-RAY DIFFRACTION98.48
1.99-2.020.31181880.23153614X-RAY DIFFRACTION98.63
2.02-2.050.25562160.21983592X-RAY DIFFRACTION98.6
2.05-2.080.28361970.21343654X-RAY DIFFRACTION98.59
2.08-2.110.25771640.20413611X-RAY DIFFRACTION98.56
2.11-2.150.25711810.19893623X-RAY DIFFRACTION98.86
2.15-2.180.26032030.20063653X-RAY DIFFRACTION98.85
2.18-2.220.24231730.20123636X-RAY DIFFRACTION99.01
2.22-2.270.21912220.19913623X-RAY DIFFRACTION99.07
2.27-2.310.24141960.1893630X-RAY DIFFRACTION98.84
2.31-2.360.25951950.1963692X-RAY DIFFRACTION98.93
2.36-2.420.2581930.18713641X-RAY DIFFRACTION99.35
2.42-2.480.21691990.18813646X-RAY DIFFRACTION99.17
2.48-2.540.22621780.18913666X-RAY DIFFRACTION99.12
2.54-2.620.23582030.18663668X-RAY DIFFRACTION99.56
2.62-2.70.22441810.1883699X-RAY DIFFRACTION99.28
2.7-2.80.23171880.20163682X-RAY DIFFRACTION99.59
2.8-2.910.24761750.1993729X-RAY DIFFRACTION99.59
2.91-3.050.22782050.19823668X-RAY DIFFRACTION99.41
3.05-3.210.23612000.193692X-RAY DIFFRACTION99.29
3.21-3.410.22872180.19393698X-RAY DIFFRACTION99.69
3.41-3.670.20711980.17033724X-RAY DIFFRACTION99.67
3.67-4.040.16812010.14583744X-RAY DIFFRACTION99.75
4.04-4.620.15282010.13233768X-RAY DIFFRACTION99.7
4.62-5.820.16442050.14663809X-RAY DIFFRACTION99.9
5.82-44.920.1871910.17123952X-RAY DIFFRACTION98.97

+
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