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- PDB-9h6m: Flavin-dependent tryptophan 7-halogenase RebH in complex with 6-b... -

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Basic information

Entry
Database: PDB / ID: 9h6m
TitleFlavin-dependent tryptophan 7-halogenase RebH in complex with 6-bromo-L-tryptophan
ComponentsTryptophan 7-halogenase RebH
KeywordsFLAVOPROTEIN / flavin-dependent halogenase / tryptophan halogenase / non-native substrate / unnatural substrate
Function / homology
Function and homology information


tryptophan 7-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 7-halogenase RebH
Similarity search - Component
Biological speciesLentzea aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 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 7-halogenase RebH
B: Tryptophan 7-halogenase RebH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,21610
Polymers125,0802
Non-polymers1,1368
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-52 kcal/mol
Surface area39020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.699, 114.699, 231.427
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-847-

HOH

21A-878-

HOH

31A-914-

HOH

41B-704-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 28 or resid 30 through 528))
d_2ens_1(chain "B" and (resid 2 through 28 or resid 30 through 528))

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_11SERSERLEULEUAA2 - 2822 - 48
d_12GLYGLYHISHISAA30 - 52850 - 548
d_21SERSERLEULEUBB2 - 2822 - 48
d_22GLYGLYHISHISBB30 - 52850 - 548

NCS oper: (Code: givenMatrix: (-0.718052638519, -0.695462342139, 0.0270654573446), (-0.695822733498, 0.716488836044, -0.0497440586528), (0.0152030215083, -0.0545516130792, -0.998395207144)Vector: 4. ...NCS oper: (Code: given
Matrix: (-0.718052638519, -0.695462342139, 0.0270654573446), (-0.695822733498, 0.716488836044, -0.0497440586528), (0.0152030215083, -0.0545516130792, -0.998395207144)
Vector: 4.2968053315, 1.80889354583, 1.46048172928)

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Components

#1: Protein Tryptophan 7-halogenase RebH / FADH(2)-dependent halogenase / Flavin-dependent tryptophan halogenase RebH


Mass: 62540.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentzea aerocolonigenes (bacteria) / Gene: rebH, rbmJ / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KHZ8, tryptophan 7-halogenase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BTR / 6-BROMO-TRYPTOPHAN


Type: L-peptide linking / Mass: 283.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C11H11BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 3.52 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M HEPES pH 6.8, 1.4 M NaH2PO4/K2HPO4; 9 mg/mL RebH (10 mM Tris pH 7.4, 50 mM NaCl, 1 mM DTT); 1 uL protein + 1 uL 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: P13 (MX1) / Wavelength: 0.9198 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.65→99.332 Å / Num. obs: 38097 / % possible obs: 76.5 % / Redundancy: 17.3 % / Biso Wilson estimate: 30.8 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.642 / Rrim(I) all: 0.661 / Net I/σ(I): 6.1
Reflection shellResolution: 2.65→2.91 Å / Redundancy: 17.6 % / Rmerge(I) obs: 2.924 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1907 / CC1/2: 0.738 / Rrim(I) all: 3.012 / % possible all: 15.6

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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: 2.65→49.67 Å / SU ML: 0.2651 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2124 1931 5.07 %
Rwork0.1706 36139 -
obs0.1728 38070 76.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.46 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8480 0 62 405 8947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00168782
X-RAY DIFFRACTIONf_angle_d0.431411924
X-RAY DIFFRACTIONf_chiral_restr0.04041232
X-RAY DIFFRACTIONf_plane_restr0.00361571
X-RAY DIFFRACTIONf_dihedral_angle_d11.68163162
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.339406763915 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.242760.259119X-RAY DIFFRACTION3.56
2.72-2.790.2298100.2454307X-RAY DIFFRACTION8.94
2.79-2.870.3219300.2339776X-RAY DIFFRACTION22.67
2.87-2.970.28971080.23391684X-RAY DIFFRACTION51
2.97-3.070.27561110.24012874X-RAY DIFFRACTION83.82
3.07-3.190.2791780.22873373X-RAY DIFFRACTION99.72
3.19-3.340.25572000.21193327X-RAY DIFFRACTION99.94
3.34-3.520.22531740.18083371X-RAY DIFFRACTION100
3.52-3.740.23561730.16733405X-RAY DIFFRACTION99.94
3.74-4.020.21451740.14913371X-RAY DIFFRACTION99.92
4.02-4.430.16131740.13193407X-RAY DIFFRACTION100
4.43-5.070.18212280.12573323X-RAY DIFFRACTION99.97
5.07-6.380.19281890.1643393X-RAY DIFFRACTION99.97
6.39-49.670.17781760.16573409X-RAY DIFFRACTION99.61
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)
12.454128715840.08870114273390.543436342631.09627000447-0.5234438085852.05088068763-0.05744020235550.293813499046-0.20253829728-0.0414350636821-0.0883011061205-0.02418567308540.237666333290.05607448370960.1552516420690.2430542137380.003848795595230.02457925178020.371421775315-0.04200422712140.157845883181-4.3609161146828.5079443743-26.6049082444
21.14717790167-0.002581752304650.02679548702250.5451980536090.01393441513331.384640426840.0320105211525-0.0481878084597-0.1118787656620.0746237015212-0.0345584290536-0.08713486130730.1727370763310.196445510457-0.005486859345420.1554160879390.01198908506810.00969194144950.3688070556370.00853396035190.15800233962910.001135176833.4465496201-10.774389046
31.015255355640.02218049040030.1824031259710.1853811665910.0546351319530.5318349405050.009547386274820.1299624319940.068539502177-0.00600220680378-0.05030020084170.0172813543547-0.003317690423880.04673226917270.02858557146850.173638256145-0.00472335916260.02833362119150.3769287897580.01903200937090.1490726022810.27671422721343.1544240651-15.6040932025
40.4222238895250.422699464655-0.2902252387240.837167408282-0.5284279526014.05974026442-0.212189027783-0.120284304946-0.3240572440490.09964019126680.0605576734942-0.2390519481370.8865184365970.6881402882140.07009772654830.3661275332340.12045454635-0.0467779080650.478599944050.1157790992330.35320124517718.306727332522.7886133668-1.97794977282
51.500554180680.1366979486851.364481530320.5293286534460.5383223503122.02558237020.151185163544-0.0846650886495-0.00538509319950.262534416202-0.200612572314-0.1732866617960.0187509048070.416011317837-0.2428036960390.31059261194-0.0335748515883-0.06451978915340.3562379484830.09598330639770.12887414088-6.8466205672334.281338491329.4353136645
63.529372965520.740227674287-0.9959343912780.2543803233050.1767917783083.79654787573-0.118474914314-0.146311137268-0.4263904170590.289539665602-0.107106465125-0.03971474844350.6952692033620.2670353607580.2194779110820.379791126343-0.02280163337690.05518748176970.2609903788720.03727629276060.195073251062-18.563279855920.190200811624.1180300768
70.891567676564-1.134291570990.2158376643871.58463390750.1370376754191.29876229259-0.1337854339590.168777536064-0.448126887889-0.1357686433260.08072911623990.3654081776560.338481611905-0.4125748786750.05422638718960.295940513042-0.1486329239020.01616695264130.368129479694-0.04133920337370.179795533534-34.64705851419.24972397993.29229070872
81.409123302530.4095124640690.3796981421271.105055136490.4577366098332.06747100466-0.01882451628840.066270856868-0.2524991008780.1169338989960.01764107404530.04181441808150.4860796677640.08169729324480.0255090583890.296124758114-0.06990606748940.0505406196020.204083550996-0.006417037634210.201180390758-24.670366242715.12777201168.5471659125
90.571813308224-0.1410205224720.6531719447251.0075129457-0.1827590035141.790351795160.0277086937342-0.282462782160.07681071448820.425583317317-0.1054266432720.126246179902-0.3158660804660.1404351399630.07625769593280.345379012544-0.1187059411790.01437408194590.3486949232740.02045150286320.103833358939-14.811143772444.34234510632.8496666388
100.8656015752440.174053106453-0.2096944011110.982720330304-0.1375585707660.929094802127-0.000250913303158-0.0591690592732-0.0604377606130.189033306535-0.07148218528580.168208691040.195720927777-0.1356447121750.01415952707790.272233209715-0.08331107461480.07948470408490.2810541914540.01689576719510.137347902427-30.503583137630.222737669420.6110740303
110.3530104139450.2104733498830.4359107232570.469773715367-0.03770183303611.19383069362-0.05411599123740.1823448401610.0385961637206-0.07206735145240.0532934187810.1088096640090.0938175975298-0.0385519006911-0.01203976170170.204822085662-0.03797858289410.02372142419880.33668262818-0.001760173936990.151196872521-25.297783345331.68757238151.19361903372
122.331132352320.547081073447-1.611131294752.43560761163-1.07939962754.4881735841-0.339672224934-0.132017159201-0.476709803779-0.203830096886-0.1455810184390.1909383843571.564064680880.09805077119930.2892958558540.4970212861960.0244037711160.127812052230.296353790909-0.0276794648150.356733317231-24.92310417444.965590857114.30216999751
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 80 )AA1 - 801 - 80
22chain 'A' and (resid 81 through 201 )AA81 - 20181 - 201
33chain 'A' and (resid 202 through 492 )AA202 - 492202 - 492
44chain 'A' and (resid 493 through 528 )AA493 - 528493 - 528
55chain 'B' and (resid 2 through 37 )BB2 - 371 - 36
66chain 'B' and (resid 38 through 80 )BB38 - 8037 - 79
77chain 'B' and (resid 81 through 121 )BB81 - 12180 - 120
88chain 'B' and (resid 122 through 186 )BB122 - 186121 - 185
99chain 'B' and (resid 187 through 245 )BB187 - 245186 - 244
1010chain 'B' and (resid 246 through 381 )BB246 - 381245 - 380
1111chain 'B' and (resid 382 through 494 )BB382 - 494381 - 493
1212chain 'B' and (resid 495 through 529 )BB495 - 529494 - 528

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