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

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Basic information

Entry
Database: PDB / ID: 7qek
TitleStructure of the ligand binding domain of the antibiotic biosynthesis regulator AdmX from the rhizobacterium Serratia plymuthica A153 bound to the auxin indole-3-piruvic acid (IPA).
Componentsregulator AdmX
KeywordsTRANSCRIPTION / transcriptional regulator / andrimid / antibiotic / Serratia plymuthica
Function / homology3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID
Function and homology information
Biological speciesSerratia plymuthica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.2Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: regulator AdmX
B: regulator AdmX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1135
Polymers55,6822
Non-polymers4313
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.213, 76.036, 94.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein regulator AdmX


Mass: 27841.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ligand binding domain of AdmX / Source: (gene. exp.) Serratia plymuthica (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-3IO / 3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID


Mass: 203.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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

Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 8 / Details: Tris-HCl 0.1M pH 8.0, PEG 8000 30% / PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.25→94.13 Å / Num. obs: 18502 / % possible obs: 98.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 49.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.031 / Rrim(I) all: 0.066 / Net I/σ(I): 14.5 / Num. measured all: 83219
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
2.25-2.324.70.973792116960.6030.5041.11.599.5
9-94.133.70.015124634010.0080.01755.797.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QEJ

7qej


Resolution: 2.25→35.26 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 899 4.87 %
Rwork0.2074 17553 -
obs0.2099 18452 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.93 Å2 / Biso mean: 60.7248 Å2 / Biso min: 28.94 Å2
Refinement stepCycle: final / Resolution: 2.25→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 31 30 3249
Biso mean--59.73 53.38 -
Num. residues----406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.390.3541440.28852907305199
2.39-2.580.34571510.26322892304399
2.58-2.830.3331430.2452907305099
2.83-3.240.31011490.21592895304498
3.24-4.090.22831440.19352861300596
4.09-35.260.22491680.1893091325999
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)
11.0147-0.5431-0.68440.3799-0.63221.7888-0.12890.0489-0.0580.02710.0656-0.0382-0.1070.2236-00.3021-0.026-0.01410.3584-0.02370.3689-9.0986-6.791612.2002
20.9938-0.81360.59840.42170.31351.1180.1225-0.19360.1249-0.09160.03890.0386-0.0038-0.493400.49730.0173-0.01330.5348-0.02150.4989-36.809-6.998716.8024
30.67081.0126-0.02460.3586-0.10341.3088-0.02840.0344-0.13310.0337-0.0047-0.0173-0.1087-0.2567-00.347-0.0099-0.0590.3875-0.01010.3929-30.6333-10.206119.0304
40.7567-1.67720.25811.217-0.42870.7867-0.13880.2340.0651-0.1068-0.10030.0489-0.01070.1500.4013-0.06240.06060.3936-0.02160.3178-11.5643-9.89784.0063
51.6089-0.68230.86990.61840.30332.9682-0.0627-0.06630.06140.0601-0.118-0.0401-0.2551-0.2041-00.37110.0061-0.03410.3199-0.02120.3102-19.0553-2.079934.8189
60.82380.0915-0.44820.2302-0.79460.61670.0416-0.2699-0.11690.13380.0078-0.03610.03630.517100.50890.0939-0.08190.67910.03670.48270.4922-19.141429.8715
70.9924-0.70210.3445-0.34160.22482.28920.0347-0.16180.04220.01170.0652-0.09780.1855-0.1486-00.4105-0.0398-0.01060.27870.01680.4125-15.5645-12.946236.8462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 121 )A42 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 153 )A122 - 153
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 205 )A154 - 205
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 245 )A206 - 245
5X-RAY DIFFRACTION5chain 'B' and (resid 44 through 121 )B44 - 121
6X-RAY DIFFRACTION6chain 'B' and (resid 122 through 167 )B122 - 167
7X-RAY DIFFRACTION7chain 'B' and (resid 168 through 245 )B168 - 245

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