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- PDB-9drh: Crystal structure of Tet(X7) bound to anhydrotetracycline C10-ben... -

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Basic information

Entry
Database: PDB / ID: 9drh
TitleCrystal structure of Tet(X7) bound to anhydrotetracycline C10-benzoate ester
ComponentsTet(X7)
KeywordsOXIDOREDUCTASE/INHIBITOR / Inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology: / FLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTang, W.K. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2025
Title: C10-Benzoate Esters of Anhydrotetracycline Inhibit Tetracycline Destructases and Recover Tetracycline Antibacterial Activity.
Authors: Williford, E.E. / Xue, Y.P. / Tang, W.K. / Li, R. / Jones, K.V. / Blake, K.S. / Blaine, H.C. / Lian, X. / Stallings, C.L. / Tolia, N.H. / Dantas, G. / Wencewicz, T.A.
History
DepositionSep 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tet(X7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2223
Polymers44,9041
Non-polymers1,3182
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.730, 132.730, 57.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Tet(X7)


Mass: 44903.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-A1BDP / (6aS,7S,10aS)-9-carbamoyl-7-(dimethylamino)-8,10a,12-trihydroxy-5-methyl-10,11-dioxo-6,6a,7,10,10a,11-hexahydrotetracen-1-yl pyrimidine-2-carboxylate


Mass: 532.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24N4O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
Has protein modificationN

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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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes, pH 7.5, 0.2 M ammonium sulfate, 16% PEG 4000 and 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→19.79 Å / Num. obs: 8118 / % possible obs: 99.5 % / Redundancy: 6.79 % / Biso Wilson estimate: 121.98 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.5
Reflection shellResolution: 3.3→3.51 Å / Num. unique obs: 8117 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→19.79 Å / SU ML: 0.5723 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.395
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2914 814 10.03 %
Rwork0.2335 7304 -
obs0.2395 8118 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 149.74 Å2
Refinement stepCycle: LAST / Resolution: 3.3→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 92 0 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213041
X-RAY DIFFRACTIONf_angle_d0.45944129
X-RAY DIFFRACTIONf_chiral_restr0.0396454
X-RAY DIFFRACTIONf_plane_restr0.0051531
X-RAY DIFFRACTIONf_dihedral_angle_d13.06491161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.510.42191310.36751185X-RAY DIFFRACTION100
3.51-3.770.37771340.30281204X-RAY DIFFRACTION100
3.77-4.150.3561330.28551194X-RAY DIFFRACTION99.77
4.15-4.750.32671350.23261196X-RAY DIFFRACTION98.89
4.75-5.950.26071350.24221221X-RAY DIFFRACTION99.34
5.95-19.790.24181460.1871304X-RAY DIFFRACTION99.93
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)
10.9233842993960.570908424928-0.1648177142530.5566535742780.5168343314891.744106877090.681858286980.42492025954-0.461264907896-0.497010792929-0.2638385112440.674432803733-0.216191929217-0.555289290855-3.09508699496E-51.2381027779-0.0690380286075-0.08630610570971.296609928290.0630932595771.515751219634.47317122141-37.8414667372-3.82099654707
24.62617659177-2.98567569716-0.4611985247914.10054707773-1.616589567592.178611897210.706556042973-0.11953433965-0.1436052548190.0162101731558-0.1546870827380.787135778042-0.171335066520.1012376071580.0009660502416261.30429840912-0.4384756890210.1198544885091.16029548143-0.1501100459651.2495542699112.9427007128-43.06905627467.48072380092
30.589054379881-1.168890730390.9501503650752.33602297824-1.875740195561.493129533010.596705552419-1.1795880148-0.5002253177350.0442297629137-0.6667356895570.127533109572-0.8095998931281.24181395679-2.04267804686E-51.52955652551-0.4331643879790.02533861145141.70919329565-0.07679140450991.1474045202725.6914461838-52.047726036916.6026678366
43.19377816870.0925387601305-1.29962000588-0.008075665303540.1372394603711.602957204110.643638956547-0.4761076322810.6955800667290.303679164294-0.137509745764-0.267858229302-0.9336841916440.8056079265990.001514132328741.45706724372-0.5051920792970.1619270479631.21771951446-0.2507289282641.1526277968221.5858034966-37.08298080939.19153063716
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 66 )23 - 661 - 44
22chain 'A' and (resid 67 through 220 )67 - 22045 - 198
33chain 'A' and (resid 221 through 266 )221 - 266199 - 238
44chain 'A' and (resid 267 through 393 )267 - 393239 - 365

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