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- PDB-7xup: Crystal structure of TPe3.0 -

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Basic information

Entry
Database: PDB / ID: 7xup
TitleCrystal structure of TPe3.0
ComponentsTranscriptional regulator, PadR-like familyTranscriptional regulation
KeywordsPHOTOSYNTHESIS / triplet photoenzyme / photocatalysis / energy transfer / photocycloaddition / unnatural amino acid
Function / homologyTranscription 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 MG1363 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 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 / _citation_author.name
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


Theoretical massNumber of molelcules
Total (without water)15,1351
Polymers15,1351
Non-polymers00
Water37821
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 area7950 Å2
Unit cell
Length a, b, c (Å)69.697, 69.697, 61.787
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-221-

HOH

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Components

#1: Protein Transcriptional regulator, PadR-like family / Transcriptional regulation


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.2 M NaCl, 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: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→19.492 Å / Num. obs: 5276 / % possible obs: 97.4 % / Redundancy: 2.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.032 / Rrim(I) all: 0.056 / Χ2: 1.24 / Net I/σ(I): 19.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 557 / CC1/2: 0.887 / Rpim(I) all: 0.188 / Rrim(I) all: 0.265 / Χ2: 1.05 / % possible all: 85.9

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Processing

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

3f8f


Resolution: 2.602→19.492 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 261 4.96 %
Rwork0.2162 5000 -
obs0.2177 5261 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.95 Å2 / Biso mean: 44.3041 Å2 / Biso min: 18.51 Å2
Refinement stepCycle: final / Resolution: 2.602→19.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 0 21 923
Biso mean---36.28 -
Num. residues----110
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.602-3.27520.29171190.2402241595
3.2752-19.4920.22281420.20512585100
Refinement TLS params.Method: refined / Origin x: 11.4099 Å / Origin y: -17.5737 Å / Origin z: -8.6648 Å
111213212223313233
T0.1236 Å2-0.0709 Å20.0318 Å2-0.4258 Å2-0.0451 Å2--0.2928 Å2
L5.0374 °2-1.2406 °20.7883 °2-1.5794 °2-0.0768 °2--1.738 °2
S0.0924 Å °0.2625 Å °0.5072 Å °-0.13 Å °-0.0732 Å °0.3309 Å °-0.0606 Å °0.0232 Å °-0.001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 113
2X-RAY DIFFRACTION1allS1 - 21

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