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- PDB-9h6z: AetF, a single-component flavin-dependent tryptophan halogenase, ... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9h6z
TitleAetF, a single-component flavin-dependent tryptophan halogenase, in complex with tryptoline
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 / 2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole / AetF
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.87 Å
AuthorsBork, S. / 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.J. / Scharkowski, B. / Niemann, H.H.
History
DepositionOct 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 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)156,70511
Polymers154,1972
Non-polymers2,5089
Water16,051891
1
A: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3355
Polymers77,0991
Non-polymers1,2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3706
Polymers77,0991
Non-polymers1,2725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.048, 123.048, 87.226
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

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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 , 5 types, 900 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-WYH / 2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole


Mass: 172.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
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; 300 nL tryptoline (50 mM in H2O) dried up on plate prior crystallization

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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: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.87→123.05 Å / Num. obs: 97146 / % possible obs: 89.3 % / Redundancy: 13.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.114 / Net I/σ(I): 12.9
Reflection shellResolution: 1.87→1.96 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.77 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4768 / CC1/2: 0.752 / Rrim(I) all: 1.84 / % possible all: 35

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSBUILT=20220220data reduction
STARANISOSTARANISO 2.4.15data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.87→123.05 Å / Cross valid method: FREE R-VALUE / σ(F): 51.61 / Phase error: 27.5091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1873 4962 5.13 %
Rwork0.1667 91729 -
obs0.1697 96691 90 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.78 Å2
Refinement stepCycle: LAST / Resolution: 1.87→123.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10560 0 173 891 11624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002911176
X-RAY DIFFRACTIONf_angle_d0.620915178
X-RAY DIFFRACTIONf_chiral_restr0.04291595
X-RAY DIFFRACTIONf_plane_restr0.00531957
X-RAY DIFFRACTIONf_dihedral_angle_d13.30774158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.3506730.34471364X-RAY DIFFRACTION25.69
1.9-1.940.5371500.51952159X-RAY DIFFRACTION39.85
1.94-1.970.28321920.27843397X-RAY DIFFRACTION64.24
1.97-2.010.29282250.26784110X-RAY DIFFRACTION76.79
2.01-2.060.24792320.25364536X-RAY DIFFRACTION85.14
2.06-2.110.2532950.2364890X-RAY DIFFRACTION91.68
2.11-2.160.25622790.22945109X-RAY DIFFRACTION94.28
2.16-2.220.23242820.21655029X-RAY DIFFRACTION94.51
2.22-2.280.39142340.34434858X-RAY DIFFRACTION90.69
2.28-2.360.192830.2045081X-RAY DIFFRACTION94.72
2.36-2.440.21742570.19855110X-RAY DIFFRACTION95.21
2.44-2.540.1992600.19095097X-RAY DIFFRACTION95.15
2.54-2.650.20292360.18735120X-RAY DIFFRACTION95.58
2.65-2.790.19082890.1725082X-RAY DIFFRACTION94.57
2.79-2.970.18422430.16885109X-RAY DIFFRACTION95.18
2.97-3.20.1722800.16555109X-RAY DIFFRACTION94.8
3.2-3.520.17752770.15335122X-RAY DIFFRACTION94.87
3.52-4.030.17012710.13355120X-RAY DIFFRACTION94.97
4.03-5.080.13722930.10655118X-RAY DIFFRACTION94.53
5.08-123.050.18652470.16165273X-RAY DIFFRACTION95.42
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)
11.89506982637-0.374184106508-0.8686354839281.53804828470.9471688027551.068926431060.0328814911383-0.1196805241530.1142855159350.05929169208590.314239362688-0.666455197107-0.05471565010670.325809128023-0.3818439241570.3179913149660.0310544081418-0.1020375064950.33761911898-0.0411610916230.42904547636450.867302241-9.01192814349-38.6472680635
24.237850340221.05022014087-1.213618653381.682340652760.03204758189011.54533607852-0.07632066647520.0402321800546-0.1364381433380.143249851895-0.0168595535388-0.03549734303580.2123862768630.04952451938270.1124447386680.2379363683210.0302635730592-0.04546925931420.2180131013010.0114714284720.18294795813748.7169562809-43.233110577413.5575760737
36.969088774224.034844718842.003383749923.085361719270.9085873201272.59166362325-0.0157528078487-0.286501957891-0.2177087108220.298545106968-0.119634686066-0.06686647851440.35692386835-0.1482751470930.09910659980980.2996492629340.01760486497460.0620425362080.162314030583-0.06430465647690.1942497890641.5802744555-51.909698201313.9186289211
40.666841391512-0.0383021778542-0.1504319785370.1693319893580.1617533143190.348561707925-0.01556267405210.05447243527720.0219588866909-0.0510648881192-0.0445472819565-0.01491143478860.000387244957806-0.01994428050580.05297808316740.2985515395560.00530210816506-0.01269386968810.2865344134640.002939868045040.28389417322157.9916086005-38.5977391088-8.04080830161
50.2302514224720.607586109621-0.08427470548092.20971217865-0.1554429662420.391207298511-0.006705462998750.08781334590450.00141462428321-0.0618038210633-0.0568067950760.29445756270.113243178977-0.1123149496620.07044137117430.2584898121580.0106981042449-0.0153758741130.300346389718-0.08165029035060.29682557277132.8078624462-45.06803625970.227565618952
61.297598269180.5298561774340.1422975612291.14233084496-0.02330027195291.121141586810.06664242838520.01266449717160.08435345333960.0416515474543-0.1297057358110.125733806697-0.0349935053066-0.0688760886350.07500498972550.1841561267320.0279243917227-0.003599477733730.235677664655-0.06615952438410.27518916632636.3034777567-29.18374420356.42191767981
71.08658755647-0.0238780468756-1.743082601661.02465660945-0.4768711097833.06900836120.1465871506520.03365141530430.148890649168-0.0661470152365-0.005023562159640.105450259411-0.25929498136-0.0555064216408-0.1460589905010.275016102345-0.0361296346664-0.03639962068210.241863189311-0.01491509219140.35820614699956.1245922414-17.1934625048-1.50267085227
80.8236307661140.382736291137-0.3568855547120.4371036952760.3667906956842.54612879612-0.1322971017270.02602959317340.077506590759-0.1543348063290.0531435328503-0.2232580976950.2461852328820.2468678363570.08730819465430.2584715583710.004648113131590.02742641178790.3646903942140.05032685387670.32027114238477.8277069185-41.3768241461-11.5603074386
92.22120116218-1.13491624446-2.465016640672.362629940682.05481668393.369400648410.252870909833-0.08903189216980.484974752647-0.3881724718670.0741574704788-0.28776209624-0.6347100969790.261932228791-0.3118284601930.410834731403-0.0251205599706-0.04839460806680.3047334816320.0894776929560.41938460025663.838931689-13.8276440463-10.0409681748
102.024931562840.195003997032-0.3149529971062.335181323480.300935217911.468521495090.08777075274040.2942558837120.856531419934-0.108744218419-0.008317379347680.375782171589-0.451106635753-0.100741411484-0.01366166230760.423533680710.0882379962873-0.007569460933750.266524195067-0.02222661616010.58997390652838.6567409063-9.510937785072.51938452125
112.210432999240.953110427456-0.4368753445053.430254773410.9884178468281.517701744240.07439502596450.2633748871750.0503061467668-0.0220287231506-0.07283900242280.0890312182092-0.110959695413-0.337232729494-0.01009533554710.2896753981450.0445292217727-0.02107417487520.3476517989530.01085150123320.18961913717119.9108627551-11.7356156793-56.7479638566
122.931145378614.16334408722-0.9819708707798.19055822286-2.196444173132.429087902240.02501048768040.309087953824-0.00775234381239-0.392423835324-0.08245446555920.3109237458860.121606616597-0.3968039911160.05570316452130.2152003122520.0442786334091-0.008699741960440.417463069139-0.09272773108610.23461433091711.2612803908-18.9821499459-57.1301780678
130.1091019145240.0506690574821-0.1333065939932.644440804021.257073675310.93379772209-0.08143234526190.0792364182498-0.003818183893760.117306806437-0.1093952801440.5728257590090.0926535533458-0.2735519546850.1792602709360.289988263747-0.0396729250085-0.01186038437590.39649647225-0.0525733637570.3701641949248.28196227518-11.5919560739-46.0714353636
141.81396964776-1.43548855403-0.802681964822.12998919631.00053900051.596393322090.1157496640350.04738542672970.1480290846740.04678542138250.0277765060566-0.237595274209-0.047903366485-0.0395697782566-0.1453788417590.28244829757-0.0290224092823-0.02576386909810.278447409016-0.03700485934620.25663886067224.67935527042.0712570824-35.2347612497
150.464035484913-0.182912874643-0.3459698855680.8308209526620.3402737126140.593262643330.0628642669277-0.0193305515850.004958275140280.09299681226710.00970162613395-0.06330230960610.000505524667860.0336663612977-0.06674913734120.286841071903-0.00886594117935-0.01957535469590.256820425129-0.02618861203610.2223526919426.8464137307-2.0540143775-32.2041947217
165.842308554621.77573331041-0.9204265382010.687788410874-0.8088906699721.87822757358-0.100340846358-0.0262292342493-0.3801035165790.180831960568-0.03260331591580.06935284948150.286621549458-0.2333522291170.1250884552430.276929164383-0.03057259335010.02902125084760.228834244231-0.06086788611760.21253745531818.14569622-27.7241795367-43.3616585417
171.78889943030.233510878115-0.5457793825161.507529106610.2110126286671.6580482111-0.0405671071899-0.0346491844322-0.1782417182530.021277310680.0254848548632-0.09430669907680.09326815019420.001615852419970.01885674669380.225075141336-0.001667246207-0.0008256369940680.188885656077-0.04697725691440.24098226801234.0082506278-23.8728788145-49.0592307208
180.827852070651-0.54107352361-0.5368140714581.170686955981.708888418393.451877122370.138706658601-0.09842700847220.0834401081822-0.01731534436060.204921843431-0.378222141642-0.01072099619130.395978458896-0.3586206424370.27623267778-0.05617538873690.02414875181040.296680323907-0.07395013695310.40221395846744.8842069321-3.37982588964-41.3614110853
190.7098441846120.567800399647-0.3702771000811.414405987310.1539146527944.001863714330.1820541973880.01443386194080.261282881934-0.01759356309750.01830161379870.0403880659431-0.445877756815-0.317746729708-0.1689837923790.4453937041620.02202809554130.02468153784140.25231347839-0.02169397401220.32891191043419.677418601617.0985140067-31.6957680934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 569 through 655 )BF569 - 655569 - 637
22chain 'A' and (resid 1 through 75 )AA1 - 751 - 75
33chain 'A' and (resid 76 through 113 )AA76 - 11376 - 113
44chain 'A' and (resid 114 through 334 )AA114 - 334114 - 334
55chain 'A' and (resid 335 through 375 )AA335 - 375335 - 375
66chain 'A' and (resid 376 through 479 )AA376 - 479376 - 479
77chain 'A' and (resid 480 through 530 )AA480 - 530480 - 530
88chain 'A' and (resid 531 through 568 )AA531 - 568531 - 568
99chain 'A' and (resid 569 through 601 )AA569 - 601569 - 601
1010chain 'A' and (resid 602 through 655 )AA602 - 655602 - 637
1111chain 'B' and (resid 1 through 75 )BF1 - 751 - 75
1212chain 'B' and (resid 76 through 113 )BF76 - 11376 - 113
1313chain 'B' and (resid 114 through 148 )BF114 - 148114 - 148
1414chain 'B' and (resid 149 through 199 )BF149 - 199149 - 199
1515chain 'B' and (resid 200 through 334 )BF200 - 334200 - 334
1616chain 'B' and (resid 335 through 375 )BF335 - 375335 - 375
1717chain 'B' and (resid 376 through 479 )BF376 - 479376 - 479
1818chain 'B' and (resid 480 through 530 )BF480 - 530480 - 530
1919chain 'B' and (resid 531 through 568 )BF531 - 568531 - 568

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