[English] 日本語
Yorodumi
- PDB-8zf1: Crystal structure of a Chemo Triplet Photoenzyme (CTPe) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zf1
TitleCrystal structure of a Chemo Triplet Photoenzyme (CTPe)
ComponentsTranscriptional regulator, PadR-like family
KeywordsPHOTOSYNTHESIS / aritificial enzyme / protein modification / biocatalysis / energy transfer
Function / homology: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / : / Transcriptional regulator, PadR-like family
Function and homology information
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, X. / Qian, J.Y. / Guo, J. / Wu, Y.Z. / Zhong, F.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21807088 China
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Chemogenetic Evolution of Diversified Photoenzymes for Enantioselective [2 + 2] Cycloadditions in Whole Cells.
Authors: Guo, J. / Qian, J. / Cai, D. / Huang, J. / Yang, X. / Sun, N. / Zhang, J. / Pang, T. / Zhao, W. / Wu, G. / Chen, X. / Zhong, F. / Wu, Y.
History
DepositionMay 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2802
Polymers15,0111
Non-polymers2691
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.923, 70.923, 61.232
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

-
Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 15010.909 Da / Num. of mol.: 1 / Mutation: M8L/K55D/K59Q/N88H/F93C/W96L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Gene: llmg_0323 / Production host: Escherichia coli (E. coli) / References: UniProt: A2RI36
#2: Chemical ChemComp-U1O / N-(9-oxidanylidenethioxanthen-2-yl)ethanamide


Mass: 269.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11NO2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 1.8 M NaH2PO4/K2HPO4, pH=8.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→43.36 Å / Num. obs: 5561 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.919 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.042 / Rrim(I) all: 0.133 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 10.8 % / Rmerge(I) obs: 2.47 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 662 / CC1/2: 0.387 / Rpim(I) all: 1.132 / Rrim(I) all: 2.778 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
autoPXdata reduction
autoPXdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→35.462 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3016 277 5.02 %
Rwork0.271 --
obs0.2727 5523 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→35.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 19 0 872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.037884
X-RAY DIFFRACTIONf_angle_d1.6331186
X-RAY DIFFRACTIONf_dihedral_angle_d23.404334
X-RAY DIFFRACTIONf_chiral_restr0.461127
X-RAY DIFFRACTIONf_plane_restr0.005152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-3.27540.39741270.37512592X-RAY DIFFRACTION99
3.2754-35.4620.281500.24362654X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.7278 Å / Origin y: 22.5701 Å / Origin z: -8.9693 Å
111213212223313233
T0.4548 Å2-0.2265 Å20.0189 Å2-0.8161 Å2-0.1431 Å2--0.5092 Å2
L5.0021 °2-3.3203 °2-0.0474 °2-3.5521 °2-1.1791 °2--1.4707 °2
S0.1502 Å °0.0175 Å °0.4281 Å °-0.3024 Å °-0.1612 Å °0.1111 Å °0.0255 Å °0.1752 Å °0.1095 Å °
Refinement TLS groupSelection details: all

+
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