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- PDB-29oi: AetF, a single-component flavin-dependent tryptophan halogenase, ... -

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Basic information

Entry
Database: PDB / ID: 29oi
TitleAetF, a single-component flavin-dependent tryptophan halogenase, in complex with 8-bromotryptoline
ComponentsAetF
KeywordsFLAVOPROTEIN / single-component halogenase / tryptophan halogenase / non-native substrate / unnatural substrate
Function / homologyFAD/NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / : / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / AetF
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å
AuthorsHorstmeier, H. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 694/10-1 Germany
CitationJournal: To Be Published
Title: Structural basis of regioselective double halogenation of the beta-carboline tryptoline by the single-component halogenase AetF
Authors: Bork, S. / Horstmeier, H. / Scharkowski, B. / Niemann, H.H.
History
DepositionMar 26, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AetF
B: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,28920
Polymers154,1972
Non-polymers3,09218
Water12,520695
1
A: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5259
Polymers77,0991
Non-polymers1,4278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,76411
Polymers77,0991
Non-polymers1,66510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.476, 122.476, 86.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 1 through 17 or resid 19...
d_2ens_1(chain "B" and (resid 1 through 17 or resid 19...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETVALVALAA1 - 179 - 25
d_12GLUGLUTYRTYRAA19 - 34627 - 354
d_13TYRTYRTHRTHRAA348 - 392356 - 400
d_14PROPROALAALAAA394 - 513402 - 521
d_15TRPTRPSERSERAA515 - 608523 - 616
d_16LYSLYSSERSERAA629 - 655637 - 663
d_17FADFADFADFADAC701
d_18A1J4BA1J4BA1J4BA1J4BAD702
d_19PEGPEGPEGPEGAE703
d_110EDOEDOEDOEDOAF704
d_111EDOEDOEDOEDOAG705
d_112EDOEDOEDOEDOAH706
d_113EDOEDOEDOEDOAI707
d_21METMETVALVALBB1 - 179 - 25
d_22GLUGLUTYRTYRBB19 - 34627 - 354
d_23TYRTYRTHRTHRBB348 - 392356 - 400
d_24PROPROALAALABB394 - 513402 - 521
d_25TRPTRPSERSERBB515 - 655523 - 663
d_26FADFADFADFADBK701
d_27A1J4BA1J4BA1J4BA1J4BBL702
d_28PEGPEGPEGPEGBM703
d_29EDOEDOEDOEDOBN704
d_210EDOEDOEDOEDOBO705
d_211EDOEDOEDOEDOBP706
d_212EDOEDOEDOEDOBQ707

NCS oper: (Code: givenMatrix: (0.039818981996764, 0.99880261657494, -0.028421502349501), (0.99918155237855, -0.040004502365345, -0.0059887542020743), (-0.0071185714250232, -0.028159774742749, -0. ...NCS oper: (Code: given
Matrix: (0.039818981996764, 0.99880261657494, -0.028421502349501), (0.99918155237855, -0.040004502365345, -0.0059887542020743), (-0.0071185714250232, -0.028159774742749, -0.99957808750858)
Vector: 58.315456770298, -63.719414027144, -41.498063644008)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AetF


Mass: 77098.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aetokthonos hydrillicola Thurmond2011 (bacteria)
Gene: aetF / Plasmid: pET24+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B9Z9

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Non-polymers , 7 types, 713 molecules

#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: Chemical ChemComp-A1J4B / 8-bromanyl-2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole


Mass: 251.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11BrN2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Morpheus single reagent (condition A6, Morpheus Green Screen, Molecular Dimensions); 30 mM CaCl2, 30 mM MgCl2, 0.1 M HEPES/MOPS pH 7.5, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000; 6 ...Details: Morpheus single reagent (condition A6, Morpheus Green Screen, Molecular Dimensions); 30 mM CaCl2, 30 mM MgCl2, 0.1 M HEPES/MOPS pH 7.5, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000; 6 mg/mL AetF (50 mM HEPES pH 7.0, 100 mM NaCl, 1 mM DTT); 300 nL protein + 300 nL reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Nov 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.78→36.9 Å / Num. obs: 121870 / % possible obs: 99.6 % / Redundancy: 12.7 % / Biso Wilson estimate: 36.26 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.078 / Net I/σ(I): 17.17
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.54 / Num. unique obs: 19464 / CC1/2: 0.686 / Rrim(I) all: 1.446 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDSBUILT=20250430data reduction
XSCALEBUILT=20250430data scaling
PHENIX2.0_5936phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.78→36.9 Å / SU ML: 0.1989 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1844 5943 4.88 %
Rwork0.1623 115919 -
obs0.1633 121862 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.6 Å2
Refinement stepCycle: LAST / Resolution: 1.78→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10545 0 199 695 11439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411070
X-RAY DIFFRACTIONf_angle_d0.669314995
X-RAY DIFFRACTIONf_chiral_restr0.0451576
X-RAY DIFFRACTIONf_plane_restr0.00691931
X-RAY DIFFRACTIONf_dihedral_angle_d12.60494187
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.8829537768204 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.35212140.31173738X-RAY DIFFRACTION98.16
1.8-1.820.30331740.27493867X-RAY DIFFRACTION100
1.82-1.840.29531850.23973856X-RAY DIFFRACTION98.8
1.84-1.870.25271760.22143880X-RAY DIFFRACTION99.83
1.87-1.890.23891810.21613800X-RAY DIFFRACTION99.1
1.89-1.920.24552010.20263871X-RAY DIFFRACTION99.24
1.92-1.940.22041730.19713856X-RAY DIFFRACTION99.93
1.94-1.970.25662020.19143847X-RAY DIFFRACTION99.22
1.97-20.20272210.18753808X-RAY DIFFRACTION99.63
2-2.040.21672100.18053858X-RAY DIFFRACTION99.83
2.04-2.070.22651810.17053808X-RAY DIFFRACTION99.28
2.07-2.110.21521800.16453912X-RAY DIFFRACTION99.27
2.11-2.150.1821950.15853845X-RAY DIFFRACTION99.73
2.15-2.190.20221710.15453865X-RAY DIFFRACTION99.58
2.19-2.240.1742060.14773841X-RAY DIFFRACTION99.73
2.24-2.290.19411990.15473840X-RAY DIFFRACTION99.73
2.29-2.350.20021830.15493905X-RAY DIFFRACTION99.8
2.35-2.410.20732020.15813857X-RAY DIFFRACTION99.83
2.41-2.480.1912130.15383840X-RAY DIFFRACTION99.88
2.48-2.560.192000.16493871X-RAY DIFFRACTION99.93
2.56-2.660.20222170.15913873X-RAY DIFFRACTION99.95
2.66-2.760.19491940.15853876X-RAY DIFFRACTION99.9
2.76-2.890.16892150.16013884X-RAY DIFFRACTION99.98
2.89-3.040.19091760.16983872X-RAY DIFFRACTION99.78
3.04-3.230.18132330.16523852X-RAY DIFFRACTION99.88
3.23-3.480.17212050.15583905X-RAY DIFFRACTION99.95
3.48-3.830.18351980.1563900X-RAY DIFFRACTION100
3.83-4.380.15272120.13673897X-RAY DIFFRACTION100
4.38-5.520.14761980.14093933X-RAY DIFFRACTION100
5.52-36.90.19622280.18913962X-RAY DIFFRACTION99.64
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)
12.92298468452960.77884802859978-0.0912559050831482.2131251647510.553920539816550.90822719275758-0.014516365257779-0.18541779992754-0.241012896085630.32122222527596-0.0460704299768060.0464968197556260.37953820025562-0.00674338057749660.0633620175358290.473516693488360.0395136091004220.0197036544463590.304673980956530.0208928315718760.2206679816052246.843204147615-44.6307724997514.548265093551
21.1997265767544-0.063826570363344-0.456587786899620.513650137213220.322315139877540.74452151070917-0.0643822353870920.0671176892324990.0336206538785230.076450573700630.0235547346953430.0443764462844010.040554106449858-0.028457364081650.0484819948375030.31229179709825-0.0082229112867258-0.0110599039685810.300186214103640.01350479310960.2455850477268254.672721647766-38.766765729895-6.1556213900033
32.21772644722560.30720148557644-0.217528983446052.11346684639190.41505119042281.8148617290670.0195021277620140.0364202516918840.227104331056290.00019372793912371-0.0698973528175250.27992942449337-0.021750931652764-0.116647558599530.0574868800712330.265427665303570.0224389542892040.0193182862705380.28143239267737-0.0266708121091960.3016298272153537.758089842468-27.264793214986.7805625038706
41.5243722195811-0.4020478628838-0.95439427469691.05350543115730.539649374207941.28011944039610.15578841661880.0304988025255950.45665785120884-0.131265872179550.036674064283291-0.088888706927705-0.340911245170890.079087456907629-0.211334922289480.34063609565907-0.0493239833682710.0043439618663720.318565787332920.0104972791400710.3856587218630760.369711123394-20.01880601544-4.5617375417429
53.16961544588041.9830829069574-0.541628545357643.18512505093350.314414917725071.2795716226312-0.125005416351240.349441971903460.076029296705588-0.116915427603210.0475882601674620.289531629264170.075452548210441-0.298126285815080.0859930014251840.30511029341640.014706628070951-0.0134501170565030.38512882015150.00263658409293670.2901654071131214.241423507849-16.20114283893-55.146727637352
60.490923520929720.066524002901838-0.14100844073290.920846601643630.198885134193050.49799323893323-0.0245308257154150.0276588270669420.00995241301373720.0376328549835-0.0317669384871650.00902677264543160.018375196344989-0.019315656183370.0641355765436130.28262695474916-0.00144274535857320.00929175577470020.283714117294740.00496469521006410.2849055648231522.85067882511-4.8706167540082-32.96049052169
71.57225000512240.34610763360496-0.161285179650441.06543127724110.140296169758711.1654019871077-0.0953223786900990.021244564346749-0.25051839268623-0.0145144743725340.019866226124828-0.141157957196890.121778827547820.0591562280300770.0717845427309940.311251092935290.0358519966031220.0595175905170980.27324595759269-0.00475471861343120.349594939384133.724570092108-21.442270360615-46.045492497074
80.989769895503040.37094342422315-0.0179465732137691.104234854773-0.114635241899772.10016332207030.062255974882481-0.110646015819840.297075942454120.078158108955197-0.05563733014991-0.07737853510808-0.3134903914863-0.060022157090809-0.00261552502300350.4119286928822-0.036924732056737-0.0236545503898410.3241399980396-0.0496306333393310.4107818246944925.03575799125213.212146156551-30.603946229894
95.1614423935649-2.453179546122-4.83872336677843.00245419007524.49865414226087.39943108721840.17338901050033-0.620564861868120.55634607081603-0.0935791372720010.34361966860464-0.56328409455425-0.550556961745410.86145877159685-0.511433880288570.42135726753321-0.046527377081399-0.0544479799614510.470842214862310.0320721335712550.4968176120649947.2430636234982.8001484297305-30.842878630561
105.13726674139481.7712869771583-0.909717461768483.7121160786483-0.637121733877742.141666733414-0.15494489939936-0.12931860498412-0.437657932929070.0938054984552110.077349093664817-1.00335190963540.0991059664139310.517038962832460.0361861462743390.388597771111810.0998206319486330.0522000440795810.46466996599015-0.0053609209070950.6043745065300951.477594243519-22.733300512099-44.19296870805
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 113 )AA1 - 1131 - 113
22chain 'A' and (resid 114 through 375 )AA114 - 375114 - 375
33chain 'A' and (resid 376 through 479 )AA376 - 479376 - 479
44chain 'A' and (resid 480 through 655 )AA480 - 655480 - 637
55chain 'B' and (resid 1 through 121 )BI1 - 1211 - 121
66chain 'B' and (resid 122 through 350 )BI122 - 350122 - 350
77chain 'B' and (resid 351 through 518 )BI351 - 518351 - 518
88chain 'B' and (resid 519 through 568 )BI519 - 568519 - 568
99chain 'B' and (resid 569 through 600 )BI569 - 600569 - 600
1010chain 'B' and (resid 601 through 655 )BI601 - 655601 - 635

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