[English] 日本語
Yorodumi
- PDB-7x80: The crystal structure of PloI4-C16M/D46A/I137V -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x80
TitleThe crystal structure of PloI4-C16M/D46A/I137V
ComponentsPloI4
KeywordsLYASE / PloI4 / mutant / 2+2 Cyclase
Function / homologyAOC barrel-like / Allene oxide cyclase-like / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesMicromonospora sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLi, M. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: Nat.Chem. / Year: 2023
Title: A cyclase that catalyses competing 2 + 2 and 4 + 2 cycloadditions.
Authors: Wang, H. / Zou, Y. / Li, M. / Tang, Z. / Wang, J. / Tian, Z. / Strassner, N. / Yang, Q. / Zheng, Q. / Guo, Y. / Liu, W. / Pan, L. / Houk, K.N.
History
DepositionMar 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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: PloI4
B: PloI4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1469
Polymers31,5012
Non-polymers6457
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-35 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.960, 174.480, 50.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

21A-401-

HOH

-
Components

#1: Protein PloI4


Mass: 15750.453 Da / Num. of mol.: 2 / Mutation: C16M/D46A/I137V
Source method: isolated from a genetically manipulated source
Details: This structure is C16M/D46A/I137V mutant. / Source: (gene. exp.) Micromonospora sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 1.4 M sodium malonate (pH 6.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.97→76.39 Å / Num. obs: 26483 / % possible obs: 97.5 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.563 / Net I/σ(I): 10.8
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 1.373 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1335

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X7Z

7x7z


Resolution: 1.97→76.39 Å / SU ML: 0.2142 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8435
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2147 1310 4.95 %
Rwork0.172 25161 -
obs0.174 26471 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.93 Å2
Refinement stepCycle: LAST / Resolution: 1.97→76.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 42 313 2526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932344
X-RAY DIFFRACTIONf_angle_d1.13143185
X-RAY DIFFRACTIONf_chiral_restr0.0631359
X-RAY DIFFRACTIONf_plane_restr0.0069417
X-RAY DIFFRACTIONf_dihedral_angle_d24.7032362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.050.28371520.21942800X-RAY DIFFRACTION99.49
2.05-2.140.2291390.19292836X-RAY DIFFRACTION99.8
2.14-2.250.25131460.19172829X-RAY DIFFRACTION99.87
2.25-2.390.2231580.19282820X-RAY DIFFRACTION99.97
2.39-2.580.24561330.19642839X-RAY DIFFRACTION99.9
2.58-2.840.2741660.1822850X-RAY DIFFRACTION99.93
2.84-3.250.19971560.16392867X-RAY DIFFRACTION100
3.25-4.090.19011090.1412282X-RAY DIFFRACTION78.52
4.09-76.390.161510.15363038X-RAY DIFFRACTION99.94

+
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