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- PDB-7qej: Structure of the ligand binding domain of the antibiotic biosynth... -

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Basic information

Entry
Database: PDB / ID: 7qej
TitleStructure of the ligand binding domain of the antibiotic biosynthesis regulator AdmX from the rhizobacterium Serratia plymuthica A153 bound to the auxin indole-3-acetic acid (IAA).
ComponentsTRANSCRIPTIONAL REGULATOR AdmX
KeywordsTRANSCRIPTION / transcriptional regulator / andrimid / antibiotic / Serratia plymuthica
Function / homology1H-INDOL-3-YLACETIC ACID
Function and homology information
Biological speciesSerratia plymuthica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGavira, J.A. / Rico-Jimenez, M. / Castellvi, A. / Krell, T. / Matilla, M.A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-103972GA- I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-116261GB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-112612GB-I00 Spain
CitationJournal: Mbio / Year: 2023
Title: Emergence of an Auxin Sensing Domain in Plant-Associated Bacteria.
Authors: Gavira, J.A. / Rico-Jimenez, M. / Ortega, A. / Petukhova, N.V. / Bug, D.S. / Castellvi, A. / Porozov, Y.B. / Zhulin, I.B. / Krell, T. / Matilla, M.A.
History
DepositionDec 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2May 1, 2024Group: 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

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR AdmX
B: TRANSCRIPTIONAL REGULATOR AdmX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0816
Polymers55,6822
Non-polymers3994
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.120, 92.145, 49.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR AdmX


Mass: 27841.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia plymuthica (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 8.5
Details: C1: 30%PEG 4K, 0.2M Mg Chloride, 0.1M Tris-HCl pH 8.50
PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.81→63.31 Å / Num. obs: 37280 / % possible obs: 99.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.037 / Rrim(I) all: 0.078 / Net I/σ(I): 10.4 / Num. measured all: 155653 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.81-1.94.30.7362334254060.6890.3950.8391.599.8
5.71-63.313.70.032483013080.9990.0180.03726.998.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF2

Resolution: 1.81→63.31 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 1767 4.75 %
Rwork0.1797 35455 -
obs0.1811 37222 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.88 Å2 / Biso mean: 45.0859 Å2 / Biso min: 16.67 Å2
Refinement stepCycle: final / Resolution: 1.81→63.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 44 141 3385
Biso mean--48.05 44.87 -
Num. residues----407
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.850.28841310.27832703283499
1.85-1.910.29391350.247526962831100
1.91-1.970.28451280.234727272855100
1.97-2.040.26351500.223926902840100
2.04-2.120.28231290.202927272856100
2.12-2.220.23991360.193727042840100
2.22-2.340.24331530.17532719287299
2.34-2.480.21011690.17827042873100
2.48-2.670.23311240.19092723284799
2.67-2.940.21551560.17672744290099
2.94-3.370.22521200.17952710283097
3.37-4.250.18171210.15292725284696
4.25-63.310.16531150.17022883299897
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)
12.9110.2188-0.35892.82330.01341.7031-0.0187-0.05760.2875-0.01720.03190.0558-0.1105-0.0401-0.01860.18250.0206-0.01990.16-0.0220.188455.849378.857-5.2139
20.90670.1757-0.39152.0797-1.06293.79920.02480.0749-0.084-0.17920.0203-0.02220.33880.0403-0.03470.18060.0238-0.03350.1701-0.02560.218960.23456.7414-8.4507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 44 through 301)A44 - 301
2X-RAY DIFFRACTION2(chain 'B' and resid 43 through 245)B43 - 245

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