[English] 日本語
Yorodumi
- PDB-7dvi: Crystal Structure of AbnU: An exo-specific intermolecular Diels-A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dvi
TitleCrystal Structure of AbnU: An exo-specific intermolecular Diels-Alderase
ComponentsAOC_like domain-containing protein
KeywordsISOMERASE / Diels ALderase
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / antibiotic biosynthetic process / isomerase activity / Allene oxide cyclase barrel-like domain-containing protein
Function and homology information
Biological speciesFrankia sp. Cc1.17 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKashyap, R. / Addlagatta, A.
Funding support India, 3items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)33/2018/MD-FTT&FTC-ANB India
Science and Engineering Research Board (SERB)EMR/2015/000461 India
Science and Engineering Research Board (SERB)CRG/2019/006013 India
CitationJournal: Commun Chem / Year: 2021
Title: Exo-selective intermolecular Diels-Alder reaction by PyrI4 and AbnU on non-natural substrates.
Authors: Kashyap, R. / Yerra, N.V. / Oja, J. / Bala, S. / Potuganti, R. / Thota, J.R. / Alla, M. / Pal, D. / Addlagatta, A.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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: AOC_like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,45323
Polymers17,0721
Non-polymers1,38222
Water1,24369
1
A: AOC_like domain-containing protein
hetero molecules

A: AOC_like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,90746
Polymers34,1442
Non-polymers2,76344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)104.437, 104.437, 67.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-369-

HOH

-
Components

#1: Protein AOC_like domain-containing protein


Mass: 17071.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frankia sp. Cc1.17 (bacteria) / Gene: CC117_14200 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A1S1R073
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1 M Imidazole, pH 7.0, 20% Ethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.974 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2→45.26 Å / Num. obs: 15158 / % possible obs: 99.9 % / Redundancy: 36.4 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.011 / Rrim(I) all: 0.065 / Net I/σ(I): 40.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0534.30.6293743010920.9760.1080.6387.698.8
8.96-45.22260.03557762220.9990.0070.03590.499.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DYV

5dyv


Resolution: 2→45.22 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.591 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 724 4.8 %RANDOM
Rwork0.1908 ---
obs0.1932 14411 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.81 Å2 / Biso mean: 36.25 Å2 / Biso min: 22.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 92 69 1236
Biso mean--56.88 46.13 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131203
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171134
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.6771590
X-RAY DIFFRACTIONr_angle_other_deg1.3261.5762604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9815141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63321.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04515181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1381512
X-RAY DIFFRACTIONr_chiral_restr0.090.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02270
LS refinement shellResolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 63 -
Rwork0.255 1028 -
all-1091 -
obs--98.91 %

+
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