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- PDB-6wg9: Crystal structure of tetracycline destructase Tet(X7) -

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Basic information

Entry
Database: PDB / ID: 6wg9
TitleCrystal structure of tetracycline destructase Tet(X7)
ComponentsTetracycline destructase Tet(X7)
KeywordsFLAVOPROTEIN / Nucleotide Binding / Oxidoreductase Activity / FAD Binding / Response to Antibiotic / Oxidation Reduction Process / ANTIBIOTIC
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKumar, H. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI12339405 United States
CitationJournal: Commun Biol / Year: 2020
Title: Tetracycline-inactivating enzymes from environmental, human commensal, and pathogenic bacteria cause broad-spectrum tetracycline resistance.
Authors: Gasparrini, A.J. / Markley, J.L. / Kumar, H. / Wang, B. / Fang, L. / Irum, S. / Symister, C.T. / Wallace, M. / Burnham, C.D. / Andleeb, S. / Tolia, N.H. / Wencewicz, T.A. / Dantas, G.
History
DepositionApr 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetracycline destructase Tet(X7)
B: Tetracycline destructase Tet(X7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6414
Polymers90,0702
Non-polymers1,5712
Water1,11762
1
A: Tetracycline destructase Tet(X7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8212
Polymers45,0351
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetracycline destructase Tet(X7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8212
Polymers45,0351
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.130, 131.970, 136.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 23 through 253 or resid 261 through 393))A23 - 253
121(chain 'A' and (resid 23 through 253 or resid 261 through 393))A261 - 393
211(chain 'B' and (resid 23 through 253 or resid 261 through 393))B23 - 253
221(chain 'B' and (resid 23 through 253 or resid 261 through 393))B261 - 393
112chain 'C'C389
212chain 'D'D389

NCS ensembles :
ID
1
2

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Components

#1: Protein Tetracycline destructase Tet(X7)


Mass: 45034.957 Da / Num. of mol.: 2 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium sulfate and 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000033 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 2.55→19.77 Å / Num. obs: 34444 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 50.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09138 / Net I/σ(I): 17.31
Reflection shellResolution: 2.55→2.641 Å / Rmerge(I) obs: 0.8967 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 3416 / CC1/2: 0.817 / Rpim(I) all: 0.3809 / Rrim(I) all: 0.9762

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A6N

4a6n


Resolution: 2.55→19.77 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.279
RfactorNum. reflection% reflection
Rfree0.2434 1673 4.86 %
Rwork0.207 --
obs0.2088 34427 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.41 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 106 62 5968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386022
X-RAY DIFFRACTIONf_angle_d0.71668160
X-RAY DIFFRACTIONf_chiral_restr0.0464903
X-RAY DIFFRACTIONf_plane_restr0.00381055
X-RAY DIFFRACTIONf_dihedral_angle_d14.61382216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.620.31721330.30042671X-RAY DIFFRACTION99.72
2.62-2.710.31761420.28162704X-RAY DIFFRACTION99.89
2.71-2.810.30661330.28562689X-RAY DIFFRACTION99.89
2.81-2.920.33471490.27932683X-RAY DIFFRACTION99.82
2.92-3.050.30771320.27722699X-RAY DIFFRACTION99.86
3.05-3.210.29181410.26882708X-RAY DIFFRACTION99.72
3.21-3.410.32041340.24862710X-RAY DIFFRACTION99.61
3.41-3.670.2231380.21992710X-RAY DIFFRACTION99.68
3.67-4.040.22811370.19032753X-RAY DIFFRACTION99.9
4.04-4.620.18531400.1532742X-RAY DIFFRACTION99.93
4.62-5.790.19921460.16052785X-RAY DIFFRACTION99.76
5.79-19.770.22241480.17422900X-RAY DIFFRACTION99.54
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)
15.202535802921.60465534421-0.09738437662183.794518581890.2030040688791.93715474331-0.1181313027340.3819400537290.10554333863-0.863958330890.0392153147258-0.25692242642-0.03144034503440.2257412079140.09963602028080.66867039402-0.01835813014940.08261187313530.491952868623-0.0521974014430.27972563397233.143897811361.318283257772.6107382996
27.773106326871.31071285381-2.007562689122.46893936082-0.5400842369683.54838644662-0.2182800345960.2200847103130.105671796132-0.3511677826810.124214925257-0.240232029878-0.02545482262510.1215930627360.1153509698130.4729762972940.02817282714910.01622856687580.364324805465-0.02957428608880.33322973486632.323155123357.879252887879.9831756545
32.763594508681.95160730253-0.5888713373815.67184939636-0.9636470525852.85982160792-0.00535812472493-0.1486508401530.02195412533240.1083682574870.07698999573620.3660246537670.152600126666-0.0681425591848-0.06473139980920.2758726885380.0473426153011-0.01715680995590.348137378077-0.05140756820060.3315695073224.182881109452.066607734793.4818161066
48.282951759975.13054390846-6.079651893616.38017008007-3.487808038415.435906700850.2386027126370.05109095552030.534648108148-0.180787198516-0.05719440881910.0205116463891-0.7281789805110.297588154942-0.4052584009980.463252187919-0.0164572858499-0.02781058835420.429900232773-0.02633369918120.42357293368728.107260683672.047106387984.7664586249
58.755966493140.1671832185751.464348010028.14423419013-2.060094848816.17137347271-0.02894435116570.3043244262290.4084547507360.1535320998530.1459570537111.10287772723-0.739415839598-0.459881904976-0.175061147870.5168102852180.1333751387110.05306313289040.300251070569-0.03147741435150.5702020929954.0778788877693.8708495051107.224297226
62.74341369485-0.4350866062071.569410007492.56388406753-0.327359158441.32727673784-0.09414975374990.1222629072990.173004777190.0613135624485-0.0224966389857-0.0820585266093-0.046230608750.324212401010.1042694495940.621452152783-0.00314058465282-0.02894414697970.358773753143-0.02070747896630.33228371535226.407725503989.9898737021114.181975775
73.95371904661-3.09789922071-0.5553105766486.388333909050.9379228595241.85728493147-0.1379580960130.03834574722250.1147808637870.1697631811750.2575824968791.03649297217-0.107566817697-0.435976507147-0.06664162249130.389788732369-0.01980805541870.06606447771530.4297300131320.05211494156070.729238088165-1.5289952529383.011917064106.061634173
86.214648896880.2868499807330.3075032896243.25473394507-0.9255596096054.273826806050.0174646839584-0.281681975944-0.3470148195930.8605428378490.0444608234534-0.1096638836460.333547892844-0.0858256818815-0.06174867107640.7075856894840.0221971518443-0.03031409972570.3438194883250.009253093058470.30614857409424.086691226171.972206378126.577646325
96.66278948916-6.25991986314.011593191648.98866120241-4.364668845025.61875941138-0.297403988950.04195249625140.01429529609050.03522439622710.2602927475560.276742908427-0.0212850382619-0.0141067896242-0.04282658185490.408269206644-0.09617163358950.02909671212840.397633119916-0.04471464896980.44251642789910.305673582777.2199991455100.481196197
105.07537623262-5.30493988575.562409483366.9352685105-4.416687891517.455683328340.08378417357280.363484150397-0.0409587936241-0.315288239405-0.01243391355410.122970950648-0.1436030327470.1740549519520.1040363248270.367964473452-0.05245105783660.05250047561730.4185805081760.01256553855060.38583695750317.481045752681.811888256898.1856217761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 187 )
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 393 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 66 )
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 138 )
7X-RAY DIFFRACTION7chain 'B' and (resid 139 through 199 )
8X-RAY DIFFRACTION8chain 'B' and (resid 200 through 299 )
9X-RAY DIFFRACTION9chain 'B' and (resid 300 through 334 )
10X-RAY DIFFRACTION10chain 'B' and (resid 335 through 393 )

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