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- PDB-8zf1: Crystal structure of a Chemo Triplet Photoenzyme (CTPe) -

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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 / : / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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