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- PDB-9h6n: Flavin-dependent tryptophan 6-halogenase Thal in complex with 6-b... -

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Basic information

Entry
Database: PDB / ID: 9h6n
TitleFlavin-dependent tryptophan 6-halogenase Thal in complex with 6-bromo-L-tryptophan
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / flavin-dependent halogenase / tryptophan halogenase / bound product / enzyme-product complex
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
6-BROMO-TRYPTOPHAN / PHOSPHATE ION / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.33 Å
AuthorsBork, S. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 694/10-1 Germany
CitationJournal: Adv.Synth.Catal. / Year: 2025
Title: Iterative Use of Regiocomplementary Flavin-Dependent Halogenases Gives Access to Unique Halogenation Patterns
Authors: Montua, N. / Scharkowski, B. / Bork, S. / Niemann, H.H. / Sewald, N.
History
DepositionOct 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,53713
Polymers120,5542
Non-polymers1,98311
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-25 kcal/mol
Surface area39870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.748, 136.748, 144.358
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 or resid 4 through 73...
d_2ens_1(chain "B" and (resid 2 or resid 4 through 73...

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_11ASPASPASPASPAA25
d_12ARGARGGLUGLUAA4 - 697 - 72
d_13ALAALATRPTRPAA76 - 8779 - 90
d_14THRTHRPROPROAA89 - 11692 - 119
d_15ALAALAASPASPAA118 - 204121 - 207
d_16GLYGLYPHEPHEAA207 - 326210 - 329
d_17HISHISGLYGLYAA328 - 452331 - 455
d_18PHEPHEPROPROAA458 - 482461 - 485
d_19ASNASNGLYGLYAA484 - 529487 - 532
d_110BTRBTRBTRBTRAC601
d_111PO4PO4PO4PO4AD602
d_21ASPASPASPASPBB25
d_22ARGARGGLUGLUBB4 - 697 - 72
d_23ALAALATRPTRPBB76 - 8779 - 90
d_24THRTHRPROPROBB89 - 11692 - 119
d_25ALAALAASPASPBB118 - 204121 - 207
d_26GLYGLYPHEPHEBB207 - 326210 - 329
d_27HISHISGLYGLYBB328 - 452331 - 455
d_28PHEPHEPROPROBB458 - 482461 - 485
d_29ASNASNGLYGLYBB484 - 529487 - 532
d_210BTRBTRBTRBTRBH601
d_211PO4PO4PO4PO4BI602

NCS oper: (Code: givenMatrix: (-0.591968968531, -0.221070402488, 0.77504878391), (-0.225600096023, -0.877753208853, -0.42267469882), (0.773742422884, -0.425061385557, 0.46972915764)Vector: 3. ...NCS oper: (Code: given
Matrix: (-0.591968968531, -0.221070402488, 0.77504878391), (-0.225600096023, -0.877753208853, -0.42267469882), (0.773742422884, -0.425061385557, 0.46972915764)
Vector: 3.51303300267, -131.755476274, -39.8187099819)

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Components

#1: Protein Tryptophan 6-halogenase


Mass: 60276.984 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
#2: Chemical
ChemComp-BTR / 6-BROMO-TRYPTOPHAN


Type: L-peptide linking / Mass: 283.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H11BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
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: 3.24 Å3/Da / Density % sol: 62.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.1 M bicine pH 8.8, 1.6 M KH2PO4/K2HPO4; 15 mg/mL Thal (10 mM Tris pH 7.4, 50 mM NaCl, 1 mM DTT); 100 nL protein + 100 nL reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.33→19.3 Å / Num. obs: 52933 / % possible obs: 81 % / Redundancy: 21 % / Biso Wilson estimate: 51.61 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.189 / Rrim(I) all: 0.194 / Net I/σ(I): 15.6
Reflection shellResolution: 2.33→2.58 Å / Redundancy: 21.1 % / Rmerge(I) obs: 2.786 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4814 / CC1/2: 0.415 / Rrim(I) all: 2.854 / % possible all: 28.3

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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: 2.33→19.29 Å / SU ML: 0.2782 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 2607 4.93 %
Rwork0.1564 50324 -
obs0.1585 52931 81.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.83 Å2
Refinement stepCycle: LAST / Resolution: 2.33→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8432 0 111 255 8798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228862
X-RAY DIFFRACTIONf_angle_d0.481612048
X-RAY DIFFRACTIONf_chiral_restr0.04211265
X-RAY DIFFRACTIONf_plane_restr0.00371573
X-RAY DIFFRACTIONf_dihedral_angle_d11.10943184
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.75446685834 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.370.194430.374719X-RAY DIFFRACTION0.64
2.37-2.420.528240.2747188X-RAY DIFFRACTION5.77
2.42-2.470.3964290.2782681X-RAY DIFFRACTION20.91
2.47-2.520.2385770.28281445X-RAY DIFFRACTION44.28
2.52-2.580.35141230.27682373X-RAY DIFFRACTION72.43
2.58-2.640.33171400.26133141X-RAY DIFFRACTION96.47
2.64-2.710.28461690.24873261X-RAY DIFFRACTION100
2.71-2.790.27281810.23463252X-RAY DIFFRACTION99.8
2.79-2.880.25451790.21223236X-RAY DIFFRACTION99.8
2.88-2.980.22821730.20563259X-RAY DIFFRACTION99.97
2.99-3.10.23671570.19663282X-RAY DIFFRACTION100
3.1-3.240.27061740.18083230X-RAY DIFFRACTION98.87
3.24-3.410.22111930.16663236X-RAY DIFFRACTION99.97
3.41-3.630.18651600.1463262X-RAY DIFFRACTION100
3.63-3.910.17811760.13223289X-RAY DIFFRACTION100
3.91-4.290.15611570.11973268X-RAY DIFFRACTION100
4.29-4.910.14221660.10813288X-RAY DIFFRACTION100
4.91-6.150.17071840.13633274X-RAY DIFFRACTION100
6.15-19.290.17731620.13883340X-RAY DIFFRACTION99.89
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)
13.24958766465-0.71944758494-3.721735351471.316164778431.752631040975.30470802125-0.0106767376652-0.2944026628330.03400816384150.07359658638340.129104261648-0.1139305695710.03756162112750.343497522169-0.10778858170.310306624395-0.0432023351701-0.009857488246760.438521136756-0.03484076334950.26925690006318.4178988786-45.1887513084-25.0733724196
20.5393652844230.110198098899-0.1280075814210.584412918404-0.08251033887180.9193440950010.0279914224407-0.1827617777040.05278606270.0637193308433-0.0392747855539-0.0134570473884-0.04841035170780.119057062253-0.00607211911740.356308155951-0.009436532679880.03381562823740.348315397828-0.02858412259890.2736111163182.91897757015-43.7587533583-19.5571977573
31.262616520760.0405215631438-0.3069398064981.069403302-0.1180243386950.7071781071630.01906546803580.03326794374340.181839074846-0.0326840287963-0.01854688934720.0448497400076-0.1359770669050.0561919229406-0.01351600278230.391726157789-0.05534188320850.03255751472020.3843680543670.003671895166520.2966728475231.25803404377-37.9239980511-30.0707001427
41.124549079120.487729098409-0.153953566081.4490373889-0.04798316276230.7136027486880.0265138162283-0.16503475193-0.09130029971780.158146259303-0.0221629730045-0.0107662539149-0.00823901155030.1887953330860.006032728208390.4170104073060.01885843854840.06334795715660.444437437229-0.004367856511610.287932417515-7.85348011846-54.0078770822-14.1310128046
57.65933619373-1.75289580501-2.632155882662.234952291530.0655298273441.40494997111-0.296135879177-0.573924170589-1.068102740570.05961820225340.00303492176711-0.03554928548560.1595564163450.3951448198420.2508001710270.4547598983990.002405508283970.05587965389490.5081173774470.1380542251030.547775126718-17.1289493126-85.2526600352-18.049667175
64.036220383460.662731374605-0.6261601816640.539795583705-0.1344922053970.805030449802-0.2848223299770.0124837599758-1.15414622684-0.1523355502640.0435571792398-0.2573440730510.1990073855190.1077883509310.1550962502630.4758893224190.01999802804120.1499907487470.341497375536-0.01012388483490.69051170441-6.58747009858-86.8999401755-30.2334689414
74.137108002230.527108548371-0.5728476357280.788456671084-0.0478267771961.6018738393-0.3282617209310.60486197832-1.30327338129-0.2182974352230.0989353950379-0.1883447765080.334418290275-0.04491370549320.05788749594930.452533654078-0.09452591658280.1489602262120.401587442139-0.1648013612340.668824674173-12.2987503784-83.9350058443-37.4590840964
84.027324087160.631082732898-0.2992915417681.13854148134-0.198567855820.514582400269-0.113982661367-0.671140406751-0.7143163810410.2084436586120.04798788576310.0146128366510.0199654037780.03341773419570.0792422039980.4417974021530.0478113002830.1052348331710.4568491450260.03554430686270.4769547790039.21352252816-76.7998254448-29.3020969994
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 223 )AA81 - 22380 - 222
33chain 'A' and (resid 224 through 428 )AA224 - 428223 - 427
44chain 'A' and (resid 429 through 529 )AA429 - 529428 - 528
55chain 'B' and (resid 2 through 80 )BF2 - 801 - 79
66chain 'B' and (resid 81 through 289 )BF81 - 28980 - 288
77chain 'B' and (resid 290 through 428 )BF290 - 428289 - 427
88chain 'B' and (resid 429 through 529 )BF429 - 529428 - 528

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