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- PDB-7xuq: Crystal structure of Tpe3.0 complexed with N-Boc-3-alkenylindole -

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Basic information

Entry
Database: PDB / ID: 7xuq
TitleCrystal structure of Tpe3.0 complexed with N-Boc-3-alkenylindole
ComponentsTranscriptional regulator, PadR-like family
KeywordsPHOTOSYNTHESIS / triplet photoenzyme / photocatalysis / energy transfer / photocycloaddition / unnatural amino acid
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 / Chem-I1A / Transcriptional regulator, PadR-like family
Function and homology information
Biological speciesLactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, X. / Qian, J.Y. / Sun, N.N. / Zhong, F.R. / Wu, Y.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807088 China
CitationJournal: Nature / Year: 2022
Title: Enantioselective [2+2]-cycloadditions with triplet photoenzymes.
Authors: Sun, N. / Huang, J. / Qian, J. / Zhou, T.P. / Guo, J. / Tang, L. / Zhang, W. / Deng, Y. / Zhao, W. / Wu, G. / Liao, R.Z. / Chen, X. / Zhong, F. / Wu, Y.
History
DepositionMay 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 7, 2022Group: 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.name
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4May 8, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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)15,5502
Polymers15,1351
Non-polymers4151
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8160 Å2
Unit cell
Length a, b, c (Å)68.764, 68.764, 60.386
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-409-

HOH

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 15135.001 Da / Num. of mol.: 1 / Mutation: M8L, K55D, K59Q, W96L
Source method: isolated from a genetically manipulated source
Details: There is an unnatural amino acid DFF inserted between ALA A 92 and GLU A 94.
Source: (gene. exp.) Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
Strain: MG1363 / Gene: llmg_0323 / Production host: Escherichia coli (E. coli) / References: UniProt: A2RI36
#2: Chemical ChemComp-I1A / dimethyl 2-[[2-methyl-1-[(2-methylpropan-2-yl)oxycarbonyl]indol-3-yl]methyl]-2-prop-2-enyl-propanedioate


Mass: 415.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, 25% (w/v) PEG3350

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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: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→59.551 Å / Num. obs: 5745 / % possible obs: 99.3 % / Redundancy: 20.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.032 / Rrim(I) all: 0.143 / Χ2: 1.01 / Net I/σ(I): 16.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 21.2 % / Rmerge(I) obs: 1.955 / Mean I/σ(I) obs: 2 / Num. unique obs: 640 / CC1/2: 0.736 / Rpim(I) all: 0.428 / Rrim(I) all: 2.001 / Χ2: 0.98 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F8F

3f8f


Resolution: 2.5→59.551 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 268 4.67 %
Rwork0.218 5468 -
obs0.2194 5736 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.08 Å2 / Biso mean: 69.2381 Å2 / Biso min: 36.82 Å2
Refinement stepCycle: final / Resolution: 2.5→59.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 30 11 965
Biso mean--65.91 55.47 -
Num. residues----113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5001-3.14990.33881430.30622710
3.1499-59.5510.21641250.19322758
Refinement TLS params.Method: refined / Origin x: -9.9601 Å / Origin y: 16.946 Å / Origin z: -8.8075 Å
111213212223313233
T0.2683 Å2-0.1182 Å2-0.0276 Å2-0.7761 Å2-0.0482 Å2--0.385 Å2
L5.3705 °2-2.477 °2-1.5359 °2-2.4335 °20.4472 °2--1.6086 °2
S0.1643 Å °0.2444 Å °-0.1606 Å °-0.0527 Å °-0.1198 Å °-0.2114 Å °-0.0612 Å °0.133 Å °-0.0688 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 116
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allS1 - 11

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