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- PDB-7e1n: Crystal structure of PhlH in complex with 2,4-diacetylphloroglucinol -

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Basic information

Entry
Database: PDB / ID: 7e1n
TitleCrystal structure of PhlH in complex with 2,4-diacetylphloroglucinol
ComponentsDUF1956 domain-containing protein
KeywordsTRANSCRIPTION / TetR-family regulator / Allosteric switching mechanism / biocontrol
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator YbiH, C-terminal / HTH-type transcriptional dual regulator CecR, C-terminal domain / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
2,4-bis[(1R)-1-oxidanylethyl]benzene-1,3,5-triol / PhlH
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, N. / Wu, J. / He, Y.X. / Ge, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970103 China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Molecular basis for coordinating secondary metabolite production by bacterial and plant signaling molecules.
Authors: Zhang, N. / Wu, J. / Zhang, S. / Yuan, M. / Xu, H. / Li, J. / Zhang, P. / Wang, M. / Kempher, M.L. / Tao, X. / Zhang, L.Q. / Ge, H. / He, Y.X.
History
DepositionFeb 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF1956 domain-containing protein
B: DUF1956 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9524
Polymers51,5232
Non-polymers4282
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-41 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.741, 106.741, 284.181
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein DUF1956 domain-containing protein / PhlH


Mass: 25761.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: phlH, C0J56_17395 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4JIX5
#2: Chemical ChemComp-ZHG / 2,4-bis[(1R)-1-oxidanylethyl]benzene-1,3,5-triol


Mass: 214.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.17 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2.8M Sodium chloride, 0.1M Sodium acetate trihydrate pH 4.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36698 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rpim(I) all: 0.051 / Net I/σ(I): 15.7
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 1822 / CC1/2: 0.854

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E1L

7e1l


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.639 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 1846 5 %RANDOM
Rwork0.174 ---
obs0.1758 34806 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.79 Å2 / Biso mean: 41.837 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20.71 Å2-0 Å2
2--1.42 Å2-0 Å2
3----4.59 Å2
Refinement stepCycle: final / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 30 213 3450
Biso mean--46.15 53.1 -
Num. residues----415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133309
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173170
X-RAY DIFFRACTIONr_angle_refined_deg1.891.6434503
X-RAY DIFFRACTIONr_angle_other_deg2.3371.5727346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55122.298161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92815567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0961521
X-RAY DIFFRACTIONr_chiral_restr0.1120.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023670
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02637
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 136 -
Rwork0.241 2507 -
all-2643 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04850.2934-0.09991.8388-0.62950.22270.0285-0.00590.0065-0.0528-0.02380.07280.02310.0452-0.00470.05360.0192-0.00850.1049-0.04240.048674.003871.6172129.6219
20.5895-0.14470.23640.0412-0.03490.37610.0144-0.00760.026-0.00510.01360.00330.03720.0422-0.0280.04730.0059-0.03450.0258-0.01210.075257.613276.3909129.2196
30.9538-0.3274-0.14190.6393-0.51090.61990.07970.04340.0381-0.059-0.02080.03190.04460.0163-0.05890.10910.0053-0.05860.0298-0.02050.054160.496668.6385121.7785
40.1936-0.10960.14580.23630.10620.35410.0519-0.0067-0.0224-0.02210.0108-0.00760.0386-0.0145-0.06260.0551-0.0087-0.03230.02930.00060.053643.96871.1331119.5815
50.9059-0.968-0.75732.2530.54840.6965-0.0722-0.1748-0.0703-0.0898-0.01780.11410.08760.19170.090.10740.0532-0.07750.07320.00230.09266.311443.4216116.1578
60.24980.0635-0.26840.0508-0.10770.3357-0.00210.0304-0.0659-0.0608-0.01380.03230.0814-0.00740.01590.12750.0321-0.09070.0256-0.04020.089451.02249.225108.0892
70.5595-0.34130.17560.3315-0.2810.37580.0830.0934-0.0205-0.0873-0.03440.0250.05640.0192-0.04860.09720.0219-0.0580.0358-0.02630.056351.159560.9872105.4108
80.4222-0.18610.17380.0957-0.11890.9650.03730.015-0.04840.0039-0.0080.01530.066-0.0423-0.02930.0886-0.0106-0.0610.0142-0.00510.056140.468863.8465117.2312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 49
2X-RAY DIFFRACTION2A50 - 107
3X-RAY DIFFRACTION3A108 - 132
4X-RAY DIFFRACTION4A133 - 223
5X-RAY DIFFRACTION5B20 - 50
6X-RAY DIFFRACTION6B51 - 114
7X-RAY DIFFRACTION7B115 - 169
8X-RAY DIFFRACTION8B170 - 224

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