[English] 日本語
Yorodumi
- PDB-7eue: Structural and mechanistic studies of a novel non-heme iron epime... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eue
TitleStructural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis.
ComponentsCupin domain-containing protein
KeywordsISOMERASE / non-heme iron epimerase/lyase
Function / homologyRmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / 3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID / : / Cupin domain-containing protein
Function and homology information
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08757062717 Å
AuthorsLi, T.L. / Li, Y.S. / Chen, M.H.
CitationJournal: Acs Catalysis / Year: 2022
Title: Structural and Mechanistic Bases for StnK3 and Its Mutant-Mediated Lewis-Acid-Dependent Epimerization and Retro-Aldol Reactions.
Authors: Chen, M.H. / Li, Y.S. / Hsu, N.S. / Lin, K.H. / Wang, Y.L. / Wang, Z.C. / Chang, C.F. / Lin, J.P. / Chang, C.Y. / Li, T.L.
History
DepositionMay 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cupin domain-containing protein
B: Cupin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1826
Polymers27,6642
Non-polymers5184
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-69 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.791, 66.791, 116.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-338-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALA(chain 'A' and (resid 12 through 24 or resid 30 through 56 or resid 58 through 128))AA12 - 2412 - 24
12PROPRO(chain 'A' and (resid 12 through 24 or resid 30 through 56 or resid 58 through 128))AA30 - 5630 - 56
13LYSLYS(chain 'A' and (resid 12 through 24 or resid 30 through 56 or resid 58 through 128))AA58 - 12758 - 127
24ALAALAchain 'B'BB12 - 2412 - 24
25PROPROchain 'B'BB30 - 5630 - 56
26LYSLYSchain 'B'BB58 - 12758 - 127

-
Components

#1: Protein Cupin domain-containing protein


Mass: 13831.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Gene: stnK3, G3260_000576 / Production host: Escherichia coli (E. coli) / References: UniProt: L7PIL3
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3IO / 3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID


Mass: 203.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic, pH 7.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.087→30 Å / Num. obs: 18506 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 30.9923688362 Å2 / Rsym value: 0.06 / Net I/σ(I): 26.74
Reflection shellResolution: 2.09→2.16 Å / Num. unique obs: 1823 / Rsym value: 0.593

-
Processing

Software
NameVersionClassification
PHENIXv1.11.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXv1.11.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J4C

6j4c


Resolution: 2.08757062717→28.9777017687 Å / SU ML: 0.23146833389 / Cross valid method: NONE / σ(F): 1.35884687413 / Phase error: 22.7555591467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232961939324 923 4.99756348476 %
Rwork0.190932481955 17546 -
obs0.192976267174 18469 99.9675236806 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.0567027247 Å2
Refinement stepCycle: LAST / Resolution: 2.08757062717→28.9777017687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 32 105 1846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008062401251981787
X-RAY DIFFRACTIONf_angle_d1.073721974252444
X-RAY DIFFRACTIONf_chiral_restr0.0837026347286282
X-RAY DIFFRACTIONf_plane_restr0.00680079839044317
X-RAY DIFFRACTIONf_dihedral_angle_d14.60430502311041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0876-2.19760.2907228939191320.2295644759592430X-RAY DIFFRACTION99.8830409357
2.1976-2.33520.2544719547731350.2114086075822468X-RAY DIFFRACTION100
2.3352-2.51540.2783378027631300.2192637661412477X-RAY DIFFRACTION100
2.5154-2.76840.254852443121320.2075906477682485X-RAY DIFFRACTION100
2.7684-3.16860.2740893569271270.2008054269432505X-RAY DIFFRACTION100
3.1686-3.99040.2263126645191320.1771420388972533X-RAY DIFFRACTION100
3.9904-28.97760.1868412042491350.1733046088892648X-RAY DIFFRACTION99.9281867145

+
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