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- PDB-8rs4: Flavin-dependent tryptophan 6-halogenase Thal in complex with try... -

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Basic information

Entry
Database: PDB / ID: 8rs4
TitleFlavin-dependent tryptophan 6-halogenase Thal in complex with tryptoline
ComponentsTryptophan 6-halogenase ThaL
KeywordsFLAVOPROTEIN / flavin-dependent / halogenase / non-native substrate / unnatural substrate / tryptoline
Function / homology
Function and homology information


tryptophan 6-halogenase / monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / 2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsBork, S. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 694/10-1 Germany
CitationJournal: Chembiochem / Year: 2025
Title: Structural Basis of Regioselective Bromination of Tricyclic Tryptoline by the Tryptophan Halogenase Thal.
Authors: Bork, S. / Besse, C. / Sewald, N. / Niemann, H.H.
History
DepositionJan 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 23, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan 6-halogenase ThaL
B: Tryptophan 6-halogenase ThaL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,29420
Polymers120,4402
Non-polymers1,85418
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homodimer in crystal monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-44 kcal/mol
Surface area39400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.590, 137.590, 144.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-1022-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 53 or resid 55...
d_2ens_1(chain "B" and (resid 2 through 53 or resid 55...

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_11ASPASPPROPROAA2 - 534 - 55
d_12LEULEUMETMETAA55 - 7157 - 73
d_13GLUGLUGLUGLUAA7375
d_14ALAALALYSLYSAA76 - 7978 - 81
d_15ALAALAALAALAAA81 - 14683 - 148
d_16THRTHRLEULEUAA148 - 181150 - 183
d_17ASNASNLYSLYSAA183 - 188185 - 190
d_18ALAALAVALVALAA190 - 194192 - 196
d_19ASPASPGLUGLUAA196 - 197198 - 199
d_110THRTHRLEULEUAA199 - 212201 - 214
d_111THRTHRGLNGLNAA214 - 306216 - 308
d_112GLUGLUASNASNAA308 - 327310 - 329
d_113VALVALVALVALAA329331
d_114PHEPHEILEILEAA331 - 365333 - 367
d_115ALAALAALAALAAA367 - 368369 - 370
d_116HISHISALAALAAA370 - 373372 - 375
d_117HISHISASPASPAA375 - 450377 - 452
d_118ASNASNPROPROAA464 - 482466 - 484
d_119ASNASNALAALAAA484 - 497486 - 499
d_120ALAALALYSLYSAA499 - 507501 - 509
d_121LYSLYSVALVALAA509 - 514511 - 516
d_122SERSERLEULEUAA516 - 524518 - 526
d_123GLNGLNHISHISAA526 - 528528 - 530
d_21ASPASPPROPROBB2 - 534 - 55
d_22LEULEUMETMETBB55 - 7157 - 73
d_23GLUGLUGLUGLUBB7375
d_24ALAALALYSLYSBB76 - 7978 - 81
d_25ALAALAALAALABB81 - 14683 - 148
d_26THRTHRLEULEUBB148 - 181150 - 183
d_27ASNASNLYSLYSBB183 - 188185 - 190
d_28ALAALAVALVALBB190 - 194192 - 196
d_29ASPASPGLUGLUBB196 - 197198 - 199
d_210THRTHRLEULEUBB199 - 212201 - 214
d_211THRTHRGLNGLNBB214 - 306216 - 308
d_212GLUGLUASNASNBB308 - 327310 - 329
d_213VALVALVALVALBB329331
d_214PHEPHEILEILEBB331 - 365333 - 367
d_215ALAALAALAALABB367 - 368369 - 370
d_216HISHISALAALABB370 - 373372 - 375
d_217HISHISASPASPBB375 - 450377 - 452
d_218ASNASNPROPROBB464 - 482466 - 484
d_219ASNASNALAALABB484 - 497486 - 499
d_220ALAALALYSLYSBB499 - 507501 - 509
d_221LYSLYSVALVALBB509 - 514511 - 516
d_222SERSERLEULEUBB516 - 524518 - 526
d_223GLNGLNHISHISBB526 - 528528 - 530

NCS oper: (Code: givenMatrix: (-0.991285623964, -0.0609781520692, -0.116766761937), (-0.0646201833959, -0.547330773775, 0.834417914463), (-0.114791304639, 0.834691972556, 0.538620708226)Vector: 116. ...NCS oper: (Code: given
Matrix: (-0.991285623964, -0.0609781520692, -0.116766761937), (-0.0646201833959, -0.547330773775, 0.834417914463), (-0.114791304639, 0.834691972556, 0.538620708226)
Vector: 116.265259799, 33.8623109908, -9.56079913219)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan 6-halogenase ThaL / Trp 6-halogenase / FADH(2)-dependent tryptophan 6-halogenase


Mass: 60219.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thaL, thdH / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280, tryptophan 6-halogenase

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Non-polymers , 5 types, 576 molecules

#2: 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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 3.29 Å3/Da / Density % sol: 62.7 % / Description: hexagonal prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: reservoir: 0.1 M bicine pH 8.0, 1.6 M KH2PO4/K2HPO4; protein: 15 mg/mL Thal-wt (10 mM Tris pH 7.4, 50 mM NaCl, 1 mM DTT); Ratio: 100 nL protein + 100 nL reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 78305 / % possible obs: 100 % / Redundancy: 10.46 % / Biso Wilson estimate: 42.8 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.157 / Net I/σ(I): 15.35
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 9.48 % / Mean I/σ(I) obs: 0.99 / Num. unique obs: 5792 / CC1/2: 0.353 / Rrim(I) all: 2.56 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSBUILT=20220820data reduction
XSCALEBUILT=20220820data scaling
Coot0.9.8.1model building
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→45.04 Å / SU ML: 0.2849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 3913 5 %
Rwork0.1688 74329 -
obs0.1705 78242 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8331 0 121 558 9010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818902
X-RAY DIFFRACTIONf_angle_d1.13612107
X-RAY DIFFRACTIONf_chiral_restr0.07381264
X-RAY DIFFRACTIONf_plane_restr0.01191580
X-RAY DIFFRACTIONf_dihedral_angle_d14.56273252
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.5034097947 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.29431400.2892658X-RAY DIFFRACTION100
2.23-2.260.27621400.28342651X-RAY DIFFRACTION100
2.26-2.280.33591390.2622652X-RAY DIFFRACTION100
2.28-2.320.2991400.26852658X-RAY DIFFRACTION100
2.32-2.350.3111390.26722633X-RAY DIFFRACTION100
2.35-2.380.30381390.25732650X-RAY DIFFRACTION99.96
2.38-2.420.30751390.24542641X-RAY DIFFRACTION99.93
2.42-2.460.28431400.23812662X-RAY DIFFRACTION100
2.46-2.50.3061390.23382634X-RAY DIFFRACTION100
2.5-2.550.24361400.22292660X-RAY DIFFRACTION100
2.55-2.60.27751390.22432650X-RAY DIFFRACTION100
2.6-2.650.25951400.21392653X-RAY DIFFRACTION100
2.65-2.710.27341390.20572630X-RAY DIFFRACTION100
2.71-2.770.24011400.19222659X-RAY DIFFRACTION100
2.77-2.840.26451390.18972644X-RAY DIFFRACTION100
2.84-2.920.22291390.18792644X-RAY DIFFRACTION100
2.92-30.22591410.192674X-RAY DIFFRACTION100
3-3.10.23081390.19392645X-RAY DIFFRACTION100
3.1-3.210.24341400.19422673X-RAY DIFFRACTION100
3.21-3.340.2571400.18512649X-RAY DIFFRACTION100
3.34-3.490.22091390.16652653X-RAY DIFFRACTION99.96
3.49-3.680.18971400.15552659X-RAY DIFFRACTION100
3.68-3.910.17251410.14862673X-RAY DIFFRACTION100
3.91-4.210.15951390.12152644X-RAY DIFFRACTION100
4.21-4.630.12831410.10762673X-RAY DIFFRACTION100
4.63-5.30.10781410.11052674X-RAY DIFFRACTION100
5.3-6.670.18441400.15022668X-RAY DIFFRACTION100
6.67-45.040.17221410.14832665X-RAY DIFFRACTION97.74
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)
14.02411375607-1.18590279656-4.282815020361.155760274021.929175884965.55716637247-0.0503892399269-0.437393100212-0.1348150942570.1313747200830.114830102752-0.0373695066417-0.07850625572870.5447318263660.0309649354610.28031009665-0.0577446085282-0.0005172925439560.3979971750650.0101547106550.27124816983817.6523883327-44.6984657095-23.9200197748
20.8651454283840.197764701964-0.3788068605540.425624972523-0.1322163470641.01220962011-0.0101160782316-0.04262367900720.09753059074660.01713957642190.02774620740520.0127375712027-0.1333885182750.0322282524564-0.02266295571330.33515290744-0.005239194940640.03687354299830.3000669494770.009077256299360.2892824853921.6412343088-40.6045468778-25.6410757367
32.133429946831.538360491130.6920833783571.500334191690.6467523268291.6569397769-0.0357005074340.0212464605303-0.1667276225020.01261516642890.0364194727634-0.2040665534550.03785872250940.27023943102-0.02925242811930.4018784793610.0667771739650.04233013953640.3912771918150.01834061695370.343321017839-7.82114303107-53.6771408006-13.0681647432
45.74594082139-1.55711289418-1.879737288322.44722246541-0.2421779713772.08435417979-0.288850072025-0.375245613259-0.627952290953-0.140718662081-0.0484878393964-0.2942259490470.1099468526820.3256751575570.2289334118860.321484481477-0.004296401353590.09725715340430.3724297854210.1039456594730.424051384881-15.4801138253-85.3568471756-16.0197024292
52.739347701432.25875481781-0.4206383072663.215122529290.05436869010430.77665806182-0.418622142006-0.276631113896-1.04657455813-0.02428935408460.11376536618-0.4648789880780.2572158496510.2456891852090.2537254914490.517582542650.09455818864750.2682825504470.5287996899920.1263598973940.80656957345614.5646463301-84.0009735737-32.6870918082
63.90017782978-0.02064655418450.02970993653641.30477623916-1.188099081182.32814725351-0.1645910267570.0158673576226-0.723184445539-0.1934518956650.0250356205651-0.1331558870040.241277814209-0.03016149690690.1087545399990.382239542573-0.02988454598020.09418377838320.2826476947610.007391702301320.456677061804-21.1162473719-86.3979749004-20.6979942206
72.393642815440.750804653415-0.9235329860030.904463566512-0.2319339967461.88643096695-0.5268222562330.423788544743-1.06517558001-0.3555786334460.00866927220191-0.3034048769680.527618203514-0.07110989475440.1703862651170.561107244937-0.08197126834040.2774111902140.381234562548-0.09995275327970.665246611566-8.7994450046-87.2929723413-34.3620748746
85.984359985090.7087102855270.7896507433094.148729232610.4325022279650.14274325237-0.181654965547-0.182108513078-0.1536822292010.0289041498084-0.02257893485820.1889700664220.141035833858-0.04253202304360.1674759408730.455925851494-0.02281922452450.1460117239210.3787381438040.006833095907960.3670068950568.6613350987-71.0498638008-35.6671285495
90.9871110770721.53326391412-0.8630776404794.6724211433-3.305195338472.46813803113-0.116536149424-1.1249880242-0.9502167372880.286416028357-0.455457313494-0.2201770723250.1289091961190.4182511204560.5726250470110.517571768110.1243758120960.1562415401990.8065800586730.3919486646990.8442167271817.3324152161-84.6376615885-17.2621184749
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 80 )AA2 - 801 - 79
22chain 'A' and (resid 81 through 428 )AA81 - 42880 - 427
33chain 'A' and (resid 429 through 529 )AA429 - 529428 - 528
44chain 'B' and (resid 2 through 80 )BJ2 - 801 - 79
55chain 'B' and (resid 81 through 152 )BJ81 - 15280 - 151
66chain 'B' and (resid 153 through 243 )BJ153 - 243152 - 242
77chain 'B' and (resid 244 through 428 )BJ244 - 428243 - 427
88chain 'B' and (resid 429 through 492 )BJ429 - 492428 - 479
99chain 'B' and (resid 493 through 529 )BJ493 - 529480 - 516

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