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- PDB-8cjg: AetF, a single-component flavin-dependent tryptophan halogenase, ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8cjg
TitleAetF, a single-component flavin-dependent tryptophan halogenase, in complex with 7-bromo-L-tryptophan
ComponentsAetF
KeywordsFLAVOPROTEIN / single-component flavin-dependent halogenase / Aetokthonotoxin / single-component monooxygenase / tryptophan halogenase
Function / homologyFAD/NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 7-bromo-L-tryptophan / AetF
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGafe, S. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF.
Authors: Gafe, S. / Niemann, H.H.
History
DepositionFeb 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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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)157,22016
Polymers154,1972
Non-polymers3,02214
Water11,710650
1
A: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6289
Polymers77,0991
Non-polymers1,5298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5927
Polymers77,0991
Non-polymers1,4936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.326, 122.326, 87.163
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
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_12GLUGLUPHEPHEAA19 - 4927 - 57
d_13LEULEUVALVALAA51 - 6559 - 73
d_14ASPASPSERSERAA67 - 24875 - 256
d_15PROPROTYRTYRAA250 - 346258 - 354
d_16TYRTYRTHRTHRAA348 - 369356 - 377
d_17PROPROPROPROAA371 - 394379 - 402
d_18PHEPHEGLYGLYAA396 - 473404 - 481
d_19TYRTYRASPASPAA475 - 603483 - 611
d_110ASPASPILEILEAA605 - 606613 - 614
d_111PHEPHESERSERAA630 - 655638 - 663
d_112FADFADFADFADAC701
d_113UV3UV3UV3UV3AD702
d_114EDOEDOEDOEDOAF704
d_21METMETVALVALBB1 - 179 - 25
d_22GLUGLUPHEPHEBB19 - 4927 - 57
d_23LEULEUVALVALBB51 - 6559 - 73
d_24ASPASPSERSERBB67 - 24875 - 256
d_25PROPROTYRTYRBB250 - 346258 - 354
d_26TYRTYRTHRTHRBB348 - 369356 - 377
d_27PROPROPROPROBB371 - 394379 - 402
d_28PHEPHEGLYGLYBB396 - 473404 - 481
d_29TYRTYRASPASPBB475 - 603483 - 611
d_210ASPASPSERSERBB605 - 655613 - 663
d_211FADFADFADFADBK701
d_212UV3UV3UV3UV3BL702
d_213EDOEDOEDOEDOBN704

NCS oper: (Code: givenMatrix: (-0.0401453097468, 0.999138787317, 0.0104898896304), (0.998828121331, 0.039844381749, 0.0274737926398), (0.0270321686942, 0.011580540668, -0.999567482931)Vector: 61. ...NCS oper: (Code: given
Matrix: (-0.0401453097468, 0.999138787317, 0.0104898896304), (0.998828121331, 0.039844381749, 0.0274737926398), (0.0270321686942, 0.011580540668, -0.999567482931)
Vector: 61.4674688211, -60.5367853124, -42.5349758819)

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B9Z9

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Non-polymers , 6 types, 664 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-UV3 / 7-bromo-L-tryptophan


Mass: 283.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 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. ...Details: 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), drop with 300 nL protein + 300 nL reservoir, crystals soaked with 150 nL 7-bromo-L-tryptophan solution (sat. 7-bromo-L-tryptophan, 25 % (v/v) ethylene glycol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
Reflection twinType: merohedral / Operator: -k,-h,-l / Fraction: 0.2
ReflectionResolution: 2.3→50 Å / Num. obs: 112302 / % possible obs: 100 % / Redundancy: 7.09 % / Biso Wilson estimate: 45.8 Å2 / CC1/2: 0.988 / Rrim(I) all: 0.248 / Net I/σ(I): 7.97
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 6.71 % / Mean I/σ(I) obs: 1.64 / Num. unique obs: 18128 / CC1/2: 0.524 / Rrim(I) all: 1.206

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEMXCuBE3data collection
XDSBUILT=20220110data reduction
XDSBUILT=20220110data scaling
PHASER2.8.3phasing
Coot0.9.4.1 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.34 Å / Cross valid method: FREE R-VALUE / σ(F): 788.09 / Phase error: 25.3136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 5606 4.99 %
Rwork0.1532 106642 -
obs0.1547 112248 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10521 0 196 650 11367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002411139
X-RAY DIFFRACTIONf_angle_d0.529115104
X-RAY DIFFRACTIONf_chiral_restr0.04231584
X-RAY DIFFRACTIONf_plane_restr0.00381944
X-RAY DIFFRACTIONf_dihedral_angle_d14.18294102
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.59536875832 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.39562810.33575375X-RAY DIFFRACTION95.03
2.34-2.380.36942820.3015311X-RAY DIFFRACTION94.92
2.38-2.430.36692760.25645314X-RAY DIFFRACTION95.06
2.43-2.480.29392800.23585342X-RAY DIFFRACTION95.02
2.48-2.530.26712820.22085329X-RAY DIFFRACTION94.97
2.53-2.590.24252790.19865356X-RAY DIFFRACTION95.03
2.59-2.660.21712820.18475326X-RAY DIFFRACTION94.97
2.66-2.730.2092800.17495357X-RAY DIFFRACTION95.03
2.73-2.810.21862780.16755280X-RAY DIFFRACTION95
2.81-2.90.20472810.16265353X-RAY DIFFRACTION95.01
2.9-30.18252820.16175337X-RAY DIFFRACTION94.98
3-3.120.19552830.15545361X-RAY DIFFRACTION94.99
3.12-3.260.21232760.15365281X-RAY DIFFRACTION95.03
3.26-3.440.20432820.13925304X-RAY DIFFRACTION94.93
3.44-3.650.16822830.13025364X-RAY DIFFRACTION94.97
3.65-3.930.14182820.11735352X-RAY DIFFRACTION94.99
3.93-4.330.13012830.10455304X-RAY DIFFRACTION94.93
4.33-4.950.13092760.09745326X-RAY DIFFRACTION95.07
4.95-6.240.15912810.13165364X-RAY DIFFRACTION95.02
6.24-46.340.15492760.14455307X-RAY DIFFRACTION95.02
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)
11.747846194140.637005938233-0.3747655540571.70316725408-0.05641004951571.113336301320.007546408542080.2819278597530.0419536196107-0.152923611378-0.01584691588940.141258544499-0.0285463782435-0.3411860558280.01266867767570.1974780396580.0270274020014-0.01492718954920.268970290174-0.00765775620510.1569048476316.8457396319-14.1574771354-56.5467013901
20.477351036985-0.0224813041876-0.1804477633240.7188104037280.4586361117680.6614586466280.05941417842930.02966717621470.0196804516680.0170033224254-0.0240490234070.0300631152771-0.0272317021682-0.0512987286401-0.03167618700910.1849668499550.00484845355980.001602138022370.1690825865980.002503991567230.17167429719423.3072230059-2.51045680443-34.5854260431
31.23435764930.138505753182-0.1122950750690.9399430601910.3102164757850.881820503191-0.0100871573352-0.0426998972676-0.1099225456610.008064649517330.00701384813812-0.08529657818720.115925198367-0.0382002115936-0.004702954362160.1563278560910.01027348240440.009720698280170.132694576155-0.01773616786450.18056659130632.9073299157-21.0569013798-46.5871486705
40.41019752779-0.172079518053-0.6905096868371.232823410811.050879535371.994865204140.0912720195072-0.1844450316480.20706175944-0.06746488849670.101174945073-0.215779111758-0.2268399349720.115046266797-0.2050672741640.26490133227-0.05712805735990.02742024679250.14463392648-0.007470966282080.24352037346333.617528755110.2105685743-31.76136712
54.190883767780.221849180591-0.6348289769211.32302165059-0.2616110199441.25926246975-0.244717208367-0.0734888705524-0.3480578243030.01501902006480.361910193003-0.7237824780610.03434309184390.330926089082-0.107490328480.2686463905730.0766559546440.04316285322410.342826543364-0.131691515280.47205899180253.4394162345-19.9582059247-44.3771806895
63.392462950950.76316676439-1.115912908061.45588942790.262208502791.46599610553-0.0427102720916-0.027556969313-0.252858715240.162033448963-0.0256349498518-0.04227117526070.16525718349-0.002141567838450.07148114331240.1792782735060.0114131483936-0.02093705522150.1673619049850.0221117215990.15845845479148.2565862709-42.684442435414.3795312814
73.902725020742.039952120810.8143585960512.891079290520.2083379996842.22073983729-0.0531900850164-0.281742066067-0.169391014240.284705228996-0.112928890553-0.01041795351870.248802786519-0.2468334693430.1504468743350.2307618225940.01854366502920.05132204787110.167016411464-0.0524078264930.17426340539141.2123609383-51.634429196414.4046934424
81.910855182160.0155181342805-0.2972641589430.5004095626630.4932217927960.5258351258760.08479095307550.268055214663-0.3600671971910.0968914365712-0.204099189187-0.03274306417520.171215217057-0.1854905073010.1481879033810.2889176444280.006359398088220.008588352168490.2340978586680.01728689643580.31847311747549.521224563-53.7599580212.95021103246
90.4199566216050.103534671025-0.05256568658520.5579104904950.1587279406220.277398245970.00827968014470.04370241586180.02942690893940.004392612253890.00457483288990.01653516363140.0224801275276-0.0300209089532-0.004022817896580.1832450832880.018072404632-0.00216193859410.1994229940020.00559992320640.21345108488559.1760472901-35.4512041461-9.29948794504
100.6954999809781.72081766958-0.7322486438985.94558739906-0.8028976961981.3339874909-0.0084479593493-0.09956561811840.110214343371-0.148824794243-0.09958554068740.4625156109370.221902624127-0.1801231642220.1109388287120.1575318676310.0161829012513-0.02456851112840.223146541639-0.05798137115470.20128428713732.9440347647-44.73112395440.611206786965
111.277165009960.510208345863-0.08689064714551.139419778720.04008579103520.969941649070.0508771890863-0.009511780061860.1247421297040.0682896879852-0.1284436703510.192293397135-0.0131231793879-0.116914733870.07693310893020.1331867826780.02126554207660.01106059539850.187447331143-0.03691513833340.23342085466336.0103917099-28.9811167536.97915470857
120.9366376400180.18058542879-1.757998289631.14705456582-0.3154292508333.991928140210.123204085670.005970651893620.110191245446-0.05030720709310.02353099392010.093605435984-0.3832638101680.00973674984949-0.1638580602670.14332339934-0.0269891618256-0.04714072051660.160609777572-0.01696018504310.26231924039455.7734177134-17.1739909694-0.733102891388
131.30530577865-0.370081948654-0.6282222811640.8984796888870.3067279274990.6167273522380.06525296444320.02879254214250.273569220388-0.0457035797716-0.0109089660319-0.139345423073-0.1587034583190.0572774759406-0.06868607615150.227885496855-0.0293455154457-0.02974257893360.2140813208220.01708912730570.22092544758760.8322419795-23.1304878558-6.02433347046
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 334 )AA114 - 334114 - 334
33chain 'A' and (resid 335 through 516 )AA335 - 516335 - 516
44chain 'A' and (resid 517 through 601 )AA517 - 601517 - 601
55chain 'A' and (resid 602 through 655 )AA602 - 655602 - 637
66chain 'B' and (resid 1 through 75 )BJ1 - 751 - 75
77chain 'B' and (resid 76 through 113 )BJ76 - 11376 - 113
88chain 'B' and (resid 114 through 148 )BJ114 - 148114 - 148
99chain 'B' and (resid 149 through 334 )BJ149 - 334149 - 334
1010chain 'B' and (resid 335 through 375 )BJ335 - 375335 - 375
1111chain 'B' and (resid 376 through 479 )BJ376 - 479376 - 479
1212chain 'B' and (resid 480 through 530 )BJ480 - 530480 - 530
1313chain 'B' and (resid 531 through 655 )BJ531 - 655531 - 632

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