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- PDB-8cjd: 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: 8cjd
TitleAetF, a single-component flavin-dependent tryptophan halogenase
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 / AetF
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)156,21611
Polymers154,1972
Non-polymers2,0189
Water20,8791159
1
A: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0885
Polymers77,0991
Non-polymers9894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1286
Polymers77,0991
Non-polymers1,0295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.790, 123.790, 88.000
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 - 5527 - 63
d_13THRTHRASPASPAA57 - 14265 - 150
d_14HISHISASPASPAA144 - 197152 - 205
d_15LEULEUSERSERAA199 - 248207 - 256
d_16PROPROGLUGLUAA250 - 274258 - 282
d_17TYRTYRPROPROAA276 - 299284 - 307
d_18ASPASPARGARGAA301 - 318309 - 326
d_19PHEPHETYRTYRAA320 - 346328 - 354
d_110TYRTYRTHRTHRAA348 - 392356 - 400
d_111PROPROALAALAAA394 - 513402 - 521
d_112TRPTRPSERSERAA515 - 655523 - 663
d_113FADFADFADFADAC701
d_114EDOEDOEDOEDOAD702
d_115PEGPEGPEGPEGAE703
d_21METMETVALVALBB1 - 179 - 25
d_22GLUGLUPHEPHEBB19 - 5527 - 63
d_23THRTHRASPASPBB57 - 14265 - 150
d_24HISHISASPASPBB144 - 197152 - 205
d_25LEULEUSERSERBB199 - 248207 - 256
d_26PROPROGLUGLUBB250 - 274258 - 282
d_27TYRTYRPROPROBB276 - 299284 - 307
d_28ASPASPARGARGBB301 - 318309 - 326
d_29PHEPHETYRTYRBB320 - 346328 - 354
d_210TYRTYRTHRTHRBB348 - 392356 - 400
d_211PROPROALAALABB394 - 513402 - 521
d_212TRPTRPSERSERBB515 - 608523 - 616
d_213LYSLYSSERSERBB629 - 655637 - 663
d_214FADFADFADFADBG701
d_215EDOEDOEDOEDOBH702
d_216PEGPEGPEGPEGBI703

NCS oper: (Code: givenMatrix: (-0.0409663182138, 0.998858796239, 0.024553328655), (0.999120299695, 0.0407317851308, 0.00997739533304), (0.00896590818494, 0.0249404662364, -0.999648731122)Vector: 64. ...NCS oper: (Code: given
Matrix: (-0.0409663182138, 0.998858796239, 0.024553328655), (0.999120299695, 0.0407317851308, 0.00997739533304), (0.00896590818494, 0.0249404662364, -0.999648731122)
Vector: 64.8600855367, -59.1492895983, -42.3510844783)

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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, 1168 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1159 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
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

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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 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 145683 / % possible obs: 99.7 % / Redundancy: 14.03 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.09 / Net I/σ(I): 16.19
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 13.57 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 23109 / CC1/2: 0.692 / Rrim(I) all: 1.322 / % possible all: 98.4

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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
Starting model: ALPHAFOLD2 MODEL LOCAL INSTALLATION

Resolution: 1.7→46.86 Å / SU ML: 0.2304 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1846 7215 4.96 %
Rwork0.159 138236 -
obs0.1602 145451 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10543 0 131 1159 11833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007711055
X-RAY DIFFRACTIONf_angle_d0.844715002
X-RAY DIFFRACTIONf_chiral_restr0.05551582
X-RAY DIFFRACTIONf_plane_restr0.00761932
X-RAY DIFFRACTIONf_dihedral_angle_d13.44114074
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.25299424801 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.39882500.36954523X-RAY DIFFRACTION97.79
1.72-1.740.34422520.32774462X-RAY DIFFRACTION98.43
1.74-1.760.33312090.30764581X-RAY DIFFRACTION98.14
1.76-1.780.29392250.26714565X-RAY DIFFRACTION100
1.78-1.810.2812450.24074611X-RAY DIFFRACTION99.75
1.81-1.830.26012580.21544575X-RAY DIFFRACTION99.96
1.83-1.860.25412600.20224566X-RAY DIFFRACTION99.83
1.86-1.890.222440.19644573X-RAY DIFFRACTION99.83
1.89-1.910.23432410.18984564X-RAY DIFFRACTION99.9
1.91-1.950.20652030.18874687X-RAY DIFFRACTION100
1.95-1.980.2012540.19094569X-RAY DIFFRACTION99.92
1.98-2.020.23342650.19344582X-RAY DIFFRACTION99.94
2.02-2.050.26012340.19774644X-RAY DIFFRACTION99.98
2.05-2.10.20592050.17364612X-RAY DIFFRACTION100
2.1-2.140.20972600.1674598X-RAY DIFFRACTION100
2.14-2.190.19842450.15994579X-RAY DIFFRACTION100
2.19-2.250.18772810.1564602X-RAY DIFFRACTION99.98
2.25-2.310.18392370.15614631X-RAY DIFFRACTION99.98
2.31-2.380.22072310.15494610X-RAY DIFFRACTION100
2.38-2.450.2132350.15784603X-RAY DIFFRACTION100
2.45-2.540.18632570.15644612X-RAY DIFFRACTION100
2.54-2.640.19552080.16174634X-RAY DIFFRACTION100
2.64-2.760.18242760.15824626X-RAY DIFFRACTION100
2.76-2.910.20272160.15854605X-RAY DIFFRACTION100
2.91-3.090.19482470.16414630X-RAY DIFFRACTION100
3.09-3.330.18392400.16284637X-RAY DIFFRACTION100
3.33-3.660.16662210.14614664X-RAY DIFFRACTION99.98
3.66-4.190.15792540.12774644X-RAY DIFFRACTION100
4.19-5.280.13672400.11924678X-RAY DIFFRACTION100
5.28-46.860.15532220.16974769X-RAY DIFFRACTION99.72
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.853405257761.02369920846-1.276503518172.26375514490.1928776825011.613065735790.00517814011039-0.116268288585-0.1387920327370.234349299655-0.0890657262374-0.03365121538680.1510970442920.01152567464350.08369044040170.2676052959880.0269978748744-0.03495783442540.2485711822550.00496328289560.1772700347748.8995240176-43.062030408314.0881973313
26.564076728793.800494342011.315547319073.385335169610.7010290692042.82295504010.102671024525-0.407157279008-0.2541259631310.321472466779-0.2716755103920.07081112616230.374756895002-0.3232003799330.1807512783550.3181556626860.01533386307940.0638806020850.21397062247-0.06235432260790.23975009050541.7538768376-52.172869134814.3252673928
37.567249706330.954537081402-2.731960309210.0912463564771-0.3064563409281.183227225570.06070513773160.104199253054-0.08482620207250.0857675163341-0.142462306919-0.07122314768890.137321742484-0.07846707302690.09246162123530.3383139787020.002974809858660.01940544315780.300016164422-0.02924205733490.34066952350150.6405180398-54.19279476442.67822840017
40.846067192428-0.0978713382416-0.1978250712430.6581116018470.2305103519190.6466219802020.001464980088710.04876854479140.04570569585360.00447111618117-0.0490720523055-0.00355362450373-0.0103903167718-0.02185793506730.05015297023980.244810085944-0.00580609347192-0.01325718378140.2660321785430.01360808415640.25013458009759.8803794745-35.9196345347-9.5931803782
52.903019618264.88534484159-1.18947854548.85748216233-1.332449450371.86194339516-0.109803350274-0.000803996044862-0.0486490622572-0.225703483896-0.02011223574170.4339792493440.180991095496-0.209556478860.1010022003580.2024038271950.007834214713850.002467158634180.24581817549-0.08215292452550.27938462624332.9643564653-45.33800430960.336186562844
61.286688560420.232221596713-0.05068099095631.226686003180.3957878299241.310270735520.0643281515709-0.04048195950870.1104302931080.0416248698236-0.1397224588190.216433374326-0.0938025665419-0.1547972032070.08141331063690.218072015020.02310663285530.003964151598790.265551388001-0.05386021643230.29623356960836.5517725569-29.29438004296.72778541756
70.9264027286940.0143910935283-1.886803756451.043025205490.3218148042835.666056042570.0437379453733-0.05920308730730.194421218172-0.0682346172956-0.0343444836523-0.0243218986613-0.421432700664-0.0167059185961-0.03814490168470.250168018374-0.022052219692-0.04366586512380.226991459389-0.006496883835330.34776823629456.5031920317-17.3164347735-1.19625862244
80.4124631430260.2712258870610.1929311175450.4611520108140.8927747940225.185700014250.01174438696860.03047930809110.0159807547085-0.1043826528010.0283572461421-0.2465630608350.3211007261740.605985586964-0.04634750426350.2280156964150.02700553340190.03117119572170.3942276846180.04137950443490.34579232925778.2931442817-41.5230939762-10.7418355792
94.52974431729-4.491381419-5.12499402867.241259299666.222005027126.132968662450.486145846941-0.04884923022580.864597671348-0.4529639330320.160160159769-0.750878002014-0.6451475993880.174259096869-0.861441736830.398831604889-0.02742342832830.01695131046230.3260559137220.06845523253050.42264202850164.3170785728-13.9261055461-9.83904382022
104.370059699632.287400583411.162739135777.0811718571.45834641192.67298859705-0.08523073448490.284558063270.986183947277-0.474724383793-0.04052875364950.475127149711-0.571678126925-0.1360450663070.1234064494240.3747164300210.1061388488450.0175522345720.2981202597-0.03731109992710.47065965833738.8406101478-10.12332114492.63509937076
111.441036006290.545574718642-0.3917826200262.163979071390.3822953344031.32524832553-0.004979467175390.218867350684-0.0660663913084-0.153969607105-0.08371465103450.159431703761-0.0311121962953-0.4090851629920.09400290898860.2722483399290.0299083254035-0.01874975276720.404783706818-0.03938153632820.21680708526116.9233910971-14.4789331304-57.2502430411
120.315502050715-0.216334226025-0.3457138287490.8879176528380.5692932947220.8340149593410.03709052151970.0534861501796-0.01558683322750.0484114509712-0.04346223126230.0102007242131-0.0196869150176-0.08083170352730.006682998532020.274959842295-0.0133517314086-0.01782503556660.261774610106-0.0008914877047360.22450957130422.8232996873-4.20637014034-35.502761579
131.25308054643-0.217163360004-0.3130553230661.175678911570.502137309661.36981659235-0.0398667336612-0.0186647861155-0.1004561755820.0398887761540.0140038201528-0.1622703262960.113137492583-0.002960193377470.02288906664340.2386410144060.0103739527729-0.001166472428020.230819087832-0.0237188327180.25708236692935.152843954-20.2884937738-47.5428118463
140.537736915307-0.191048923284-0.5383165280651.497048872150.1835082687272.777284283950.19959374229-0.02192993274990.207914317957-0.0887134672036-0.0104669631618-0.127741789616-0.501343817857-0.0614703687896-0.1811261986970.404093721634-0.04718097420230.02548098381320.219642497091-0.02600501215460.29652468849625.469558929313.8634654452-32.3031064346
151.93378428494-0.0487388553471-0.7201792209581.603967909440.9291810017161.382655852430.0333726165735-0.1012446565910.0772130185682-0.002299228575950.423154784269-0.872283989122-0.02171149441290.476969191198-0.5095659375450.2965882655320.0118019942991-0.08161755034920.397422514692-0.07476215160740.4758429549851.1769602046-8.8698184989-38.9836134162
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 75 )AA1 - 751 - 75
22chain 'A' and (resid 76 through 113 )AA76 - 11376 - 113
33chain 'A' and (resid 114 through 148 )AA114 - 148114 - 148
44chain 'A' and (resid 149 through 334 )AA149 - 334149 - 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 - 635
1111chain 'B' and (resid 1 through 113 )BE1 - 1131 - 113
1212chain 'B' and (resid 114 through 347 )BE114 - 347114 - 347
1313chain 'B' and (resid 348 through 516 )BE348 - 516348 - 516
1414chain 'B' and (resid 517 through 568 )BE517 - 568517 - 568
1515chain 'B' and (resid 569 through 655 )BE569 - 655569 - 637

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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