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- PDB-4guv: TetX derivatized with Xenon -

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Basic information

Entry
Database: PDB / ID: 4guv
TitleTetX derivatized with Xenon
ComponentsTetX2 protein
KeywordsOXIDOREDUCTASE / rossmann fold / monooxygenase / xenon
Function / homology
Function and homology information


tetracycline 11a-monooxygenase / FAD binding / monooxygenase activity / response to antibiotic / cytoplasm
Similarity search - Function
Flavin-dependent monooxygenase TetX / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / XENON / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsVolkers, G. / Palm, G.J. / Panjikar, S. / Hinrichs, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX.
Authors: Volkers, G. / Damas, J.M. / Palm, G.J. / Panjikar, S. / Soares, C.M. / Hinrichs, W.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 18, 2013Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TetX2 protein
B: TetX2 protein
C: TetX2 protein
D: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,06327
Polymers178,8144
Non-polymers5,24923
Water1,67593
1
A: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9446
Polymers44,7031
Non-polymers1,2405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0407
Polymers44,7031
Non-polymers1,3366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0407
Polymers44,7031
Non-polymers1,3366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0407
Polymers44,7031
Non-polymers1,3366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.710, 80.140, 87.500
Angle α, β, γ (deg.)111.04, 90.06, 93.29
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.99983, -0.018407, 0.000508), (-0.018404, -0.999818, -0.005034), (0.0006, 0.005024, -0.999987)-28.90917, 35.8754, 55.23034
3given(-0.999824, 0.015815, 0.010096), (0.018258, 0.943987, 0.329477), (-0.00432, 0.329603, -0.94411)-32.29535, 6.80654, 63.98867
4given(-0.999946, -0.00902, -0.005178), (0.010228, -0.943074, -0.332427), (-0.001884, -0.332462, 0.943115)1.91382, -17.80342, -3.03882

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Components

#1: Protein
TetX2 protein


Mass: 44703.395 Da / Num. of mol.: 4 / Fragment: UNP residues 11-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: tetX2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q93L51
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Xe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.5 Å
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 41035 / Redundancy: 3.43 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.79
Reflection shellResolution: 2.73→2.8 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.74

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2XDO

2xdo


Resolution: 2.73→47.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 24.718 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22105 2183 5.1 %RANDOM
Rwork0.18131 ---
obs0.18332 41035 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.876 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å2-1.32 Å2-1.15 Å2
2--0.97 Å2-0.3 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.73→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11476 0 275 93 11844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211984
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.98216285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78251461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46625.594581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.808151985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6241552
X-RAY DIFFRACTIONr_chiral_restr0.1040.21788
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219128
LS refinement shellResolution: 2.73→2.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 132 -
Rwork0.3 1977 -
obs--62.45 %
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)
12.639-0.61152.08372.968-0.73844.15260.0867-0.1943-0.26730.0862-0.04760.5350.2804-0.4311-0.0390.0698-0.09740.0450.16380.01070.257-15.8467-0.868814.9502
22.71890.7841.78732.27780.30383.96390.1003-0.01360.0438-0.08030.00890.3049-0.019-0.4004-0.10920.04160.01670.03020.1452-0.02990.1343-11.03814.6579.8319
32.75360.855-0.24336.0424-0.8925.70970.10760.23390.1301-0.1968-0.068-0.39180.00060.6036-0.03960.02270.0047-0.00730.219-0.03840.193913.61454.848215.1169
45.352-1.42980.34263.7411-0.59663.0755-0.0171-0.24870.4410.29640.00780.2114-0.6899-0.28420.00930.20190.0840.06790.1512-0.05650.1745-13.658216.319414.7415
52.98881.3279-1.6942.8275-1.18024.550.16150.22210.3613-0.0621-0.20050.4946-0.3706-0.49440.0390.04870.0826-0.02580.1559-0.03220.244913.835636.413740.8444
63.0185-0.5632-1.44452.51750.53093.48690.09570.00990.01070.144-0.02410.24830.0375-0.2917-0.07160.0552-0.0344-0.0020.1586-0.05480.084818.60530.730946.0363
73.7687-0.55380.24637.7112-2.01815.85940.0677-0.2053-0.29970.1028-0.0878-0.68120.02310.60790.02010.0091-0.00720.01060.2452-0.05050.236543.257630.436440.5855
83.45690.8684-0.17263.9628-0.02242.13110.01530.2452-0.4069-0.1868-0.1150.17760.5787-0.37370.09960.1797-0.0859-0.02810.1858-0.08590.175915.9419.216440.8291
93.6637-0.28161.28993.46140.29483.15510.05290.40830.0305-0.47390.1352-0.5396-0.1580.556-0.18810.2663-0.17560.11210.2242-0.0270.2272-14.8768-23.556244.1826
103.3197-0.66711.26823.1559-0.5773.8384-0.08870.05730.249-0.11740.0973-0.3138-0.44090.478-0.00850.2165-0.15120.02050.12460.00630.1776-19.5189-20.08351.1694
114.93680.59380.43325.04211.32934.4286-0.1725-0.15690.4361-0.0745-0.03230.5264-0.3373-0.55430.20480.43890.1628-0.12840.21110.04010.3836-44.2907-17.917646.3949
124.0713-0.20211.14683.35610.76461.81240.05940.01320.7949-0.3005-0.0514-0.2242-0.95790.3379-0.0080.7137-0.26790.05160.22510.06310.4194-16.9498-7.343349.9869
133.61080.2949-1.60183.6842-0.31343.8646-0.0844-0.4487-0.18590.59250.1175-0.53170.33590.671-0.03310.38930.1927-0.10180.2397-0.05560.207219.6207-22.126811.5224
143.12490.695-1.18682.9278-0.12043.3038-0.1136-0.0981-0.37060.12960.1468-0.360.51590.4931-0.03320.31570.1941-0.02740.1547-0.00630.182614.9725-25.59184.3266
154.9063-0.70130.21285.51431.23053.4884-0.24170.1614-0.53190.16190.07820.43420.5337-0.43140.16350.5565-0.17770.18410.22170.03660.3526-9.8055-27.73659.3305
163.31280.5644-1.73882.83790.4242.85350.0038-0.1599-0.82340.376-0.0593-0.29241.08360.3750.05540.83920.2674-0.02610.27720.03080.486617.5262-38.3365.7023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 87
2X-RAY DIFFRACTION2A88 - 189
3X-RAY DIFFRACTION3A190 - 284
4X-RAY DIFFRACTION4A285 - 382
5X-RAY DIFFRACTION5B15 - 87
6X-RAY DIFFRACTION6B88 - 189
7X-RAY DIFFRACTION7B190 - 284
8X-RAY DIFFRACTION8B285 - 382
9X-RAY DIFFRACTION9C15 - 87
10X-RAY DIFFRACTION10C88 - 189
11X-RAY DIFFRACTION11C190 - 284
12X-RAY DIFFRACTION12C285 - 382
13X-RAY DIFFRACTION13D15 - 87
14X-RAY DIFFRACTION14D88 - 189
15X-RAY DIFFRACTION15D190 - 284
16X-RAY DIFFRACTION16D285 - 382

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