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- PDB-8tti: Trp-6-Halogenase BorH complexed with FAD and Trp -

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Basic information

Entry
Database: PDB / ID: 8tti
TitleTrp-6-Halogenase BorH complexed with FAD and Trp
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / halogenase / oxidoreductase
Function / homologyFlavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / TRYPTOPHAN / Tryptophan 6-halogenase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsLingkon, K. / Bellizzi, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM144877 United States
CitationJournal: Biorxiv / Year: 2023
Title: Crystallographic and thermodynamic evidence of negative cooperativity of flavin and tryptophan binding in the flavin-dependent halogenases AbeH and BorH.
Authors: Ashaduzzaman, M. / Lingkon, K. / De Silva, A.J. / Bellizzi, J.J.
History
DepositionAug 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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
C: Tryptophan 6-halogenase
D: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,03721
Polymers240,8084
Non-polymers3,22817
Water22,3931243
1
A: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7916
Polymers60,2021
Non-polymers5885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8877
Polymers60,2021
Non-polymers6856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0843
Polymers60,2021
Non-polymers8822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2765
Polymers60,2021
Non-polymers1,0744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.680, 157.410, 112.830
Angle α, β, γ (deg.)90.000, 104.060, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
Tryptophan 6-halogenase


Mass: 60202.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: borH / Production host: Escherichia coli (E. coli) / References: UniProt: M9QSI0
#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1243 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5 300 mM (NH4)2SO4 19% (w/v) PEG 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.98→54.72 Å / Num. obs: 163198 / % possible obs: 94.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 30.87 Å2 / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.135 / Rrim(I) all: 0.19 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.98-2.051.3160.62165890.11.3161.861
2.05-2.131.0360.8165760.1911.0361.46596.4
2.13-2.230.7461.1166780.3310.7461.05596.6
2.23-2.350.5241.5164650.5480.5240.74195.6
2.35-2.490.3662163750.70.3660.51894.9
2.49-2.690.262.7146060.7070.260.36884.7
2.69-2.960.1474.3167110.9350.1470.20896.5
2.96-3.390.0856.3168870.9760.0850.12197.8
3.39-4.270.0558.6164840.9860.0550.07895.1
4.27-54.720.0469.5158270.9880.0460.06590.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→54.72 Å / SU ML: 0.3649 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2701 1989 1.22 %
Rwork0.2288 160534 -
obs0.2293 162523 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.2 Å2
Refinement stepCycle: LAST / Resolution: 1.98→54.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16685 0 201 1243 18129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002817391
X-RAY DIFFRACTIONf_angle_d0.492723654
X-RAY DIFFRACTIONf_chiral_restr0.04082459
X-RAY DIFFRACTIONf_plane_restr0.00473088
X-RAY DIFFRACTIONf_dihedral_angle_d11.37946237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.43361330.38711202X-RAY DIFFRACTION92.68
2.03-2.080.39921550.356811556X-RAY DIFFRACTION94.76
2.08-2.140.34991510.324811671X-RAY DIFFRACTION95.86
2.14-2.210.33681330.304911764X-RAY DIFFRACTION96.31
2.21-2.290.31931440.286411708X-RAY DIFFRACTION95.94
2.29-2.380.33311470.273411531X-RAY DIFFRACTION94.74
2.38-2.490.34591460.261211567X-RAY DIFFRACTION95.03
2.49-2.620.32011280.243710616X-RAY DIFFRACTION86.77
2.62-2.790.28041300.230210764X-RAY DIFFRACTION88.52
2.79-30.261440.226411939X-RAY DIFFRACTION97.77
3-3.310.26951480.208311955X-RAY DIFFRACTION97.68
3.31-3.790.22141450.191611770X-RAY DIFFRACTION96.12
3.79-4.770.21721480.172611288X-RAY DIFFRACTION92.14
4.77-54.720.23291370.212811203X-RAY DIFFRACTION90.49
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)
14.13623551560.8645229670963.331995161642.342622123990.4233919578044.2026756323-0.19330740383-0.06102133579720.06492149954830.1261128982730.2249454914210.4511826251940.220723107878-0.60294083548-0.01107229342090.222024495502-0.06677502742070.09210553184570.3445554687620.0726768313350.370812982883-44.650108493346.185549613594.0452692103
22.883887403232.18006483387-1.174110855992.658969078740.4205741673271.75147307863-0.105894335732-0.21543180022-0.01439467656110.2190906525670.0854965617277-0.182553739761-0.02246324398890.109907035990.007167867930740.2250507930330.0441278631006-0.004456852697340.1642030314170.02295771404030.256511591216-13.261887900851.3500989827103.456396836
31.79509672737-0.231826063740.6570187681931.580188713850.2346435271752.50863659543-0.07830207815750.000761012111034-0.32234061776-0.04811999930520.1498408631730.338690438510.40476937487-0.488425475591-0.05590918619050.27249899248-0.1067533479170.0407713168930.2798254282380.07163473251040.455951958201-40.652452249837.294132230288.990922954
42.19091426353-0.714476538760.8615925191021.04390638642-0.4636280129061.22761370329-0.1217445091820.137069700599-0.269390795097-0.1341000313940.1979433176520.06667487945960.177598276058-0.0608521295324-0.0804096128760.249111411679-0.0622147566910.07447632125250.1812400566430.01902131887750.292517795744-25.841476133738.264489131688.2831474598
53.939349616681.487927688520.1069895530134.87181257526-0.6078324887432.82070740554-0.1095187107090.1491935304620.4976839201350.03785897292840.09885124068360.187817924274-0.168281658228-0.1656902910970.01409511537910.1771503524260.0080351758869-0.01228613716590.1402983616580.008804246687270.200418051205-15.879235540958.172814080589.6120784608
64.835414516094.36620928517-1.970144462473.77995794321-1.662541961171.833289487560.372547530566-0.5262568080770.5031409350380.518661262384-0.2447764007910.475944704844-0.319817963270.108182761618-0.118537089920.2597311956390.0523440023060.04596892189430.247278436781-0.05554008970840.317249456365-19.683960880757.8490960664111.635785301
73.955930791290.39658424463-3.369255397811.03677030722-0.5750559105984.33080946252-0.0847567260517-0.1249912613180.03855224009720.1633864127360.225546049696-0.730664402949-0.03663589044820.73723439625-0.1193935036710.257036473819-0.0120948281027-0.02572020916360.44075204863-0.2019577793530.74181196613826.7054648165159.16640071894.1802171664
82.150413895541.836673831291.000915940711.713350871550.3439976777992.39905847890.0796470311546-0.1779735225960.115025329950.147020669109-0.05226553305390.07788543163420.148976778945-0.182713168028-0.05183349104310.2029145075350.0447520362678-0.001234485590030.1638650738830.01265385265140.235123587503-4.62609332103154.006536135103.664486334
91.74934766256-0.0138529036023-0.4974665879641.342666200220.1876279297921.826101687280.0124533258078-0.001550299261840.451361921467-0.1467780225590.201762872714-0.646072535473-0.4183490981970.50530554496-0.1800666957220.320801092948-0.09675702319670.06583341692380.367517232132-0.1109375001620.76412285801622.6181742889168.01014826989.2676447692
101.39097498683-0.788621479836-0.6335459935481.302725941450.3739067293051.22681743029-0.03759238026210.03201886932850.42122461926-0.09471493086210.185699507644-0.417218767937-0.2030326956770.167797118617-0.1646251236030.226633478027-0.0312468801836-0.01510753213350.209266756627-0.02679040824250.5119511833127.99598107595166.89980329988.134388072
113.146460974421.4027455883-0.004166412893553.181146815590.9033863514922.484668770960.01275234114310.0162847593918-0.278603421021-0.05433926049910.0135694818578-0.3500503170260.1779257533550.233793950711-0.01595264710350.2146794031850.03955142053240.03466552174370.1419542771320.007816193523790.269862970767-2.25475961081147.1182412590.0362409406
124.925350172534.02402684632.270853699464.153198411421.612080727212.378409321110.448508993615-0.43441547865-0.5074076252240.752350226187-0.204528809802-0.6085699738420.441593145329-0.104218625617-0.2455721085650.3422324596650.086431252707-0.05138764599960.1974390506560.01491349727030.3202551048391.68049150071147.521783867111.908885085
136.55409451112-0.716250901958-0.3039449846372.20126450514-0.02065176514783.644896357250.044406172572-0.0753668607011-0.441595506520.001010953615130.01019634684120.1900174664160.462535664528-0.0168690001749-0.06410377045950.280477667569-0.00704902019869-0.03198215059680.135629760306-0.02853989873970.402954677321-9.50569784709122.5360280381.5005733152
143.474012468140.3939394098280.3881447412891.9960907613-0.04410694779930.9808018633410.1107865469650.0265612253195-0.5153719392710.0109848432808-0.0532901458608-0.3520241071080.3327139262970.388070658125-0.04902782652790.3376401689880.14146998452-0.0002334390749460.343595133067-0.03162086772440.4909360653322.3236593505122.08089856475.5944003415
153.26973311968-1.25824015594-0.7878497487161.622663492990.4774825930981.777919735130.1559392860540.492716319989-0.576763273412-0.264775854728-0.1364683029310.110627148560.33989898866-0.0250460333367-0.008853077735580.3172642765960.0200385710804-0.04672519832880.266958294782-0.1105990541610.412147671895-0.566603145324124.17975564667.4463725766
162.782592398251.52784387888-0.9661200136314.25317422561-0.290778737043.707722567290.2351898311730.0151935128888-0.02685424250580.542067049583-0.1690568503190.338642712386-0.142896996942-0.387323818707-0.1080457178510.2550141066270.04196147993210.07405067441330.376921021072-0.08758637022940.54267765729114.2698009096137.63646224278.2030411544
172.454384646320.943065010508-0.038531910063.235679673170.6521456253941.573745067570.14968870608-0.157322573988-0.2763855237020.3334843059380.026648647411-0.5720516185730.2613906311930.413339512074-0.1638213153670.3028275403340.09247253558110.0005715947356620.369286542446-0.06469964988570.55695214362127.4235688951127.14438945180.3072651729
184.29807441249-0.1846681512440.4885686411612.67585047688-1.069958526883.97446005331-0.176684677217-0.1868584461640.6916429048750.06283329974560.2636736666230.0387179127945-0.410791049117-0.127360584599-0.1165676542820.288177489532-0.0452633829442-0.01689666680580.2264967365590.03096044353460.709416488607-8.674731477882.924217098781.3721006443
192.065556217050.568048285019-0.6720511229952.939956712240.5110164650811.02542707451-0.005348017711430.08048183452940.942844366019-0.000822393023865-0.01969942151450.588976406627-0.328158442997-0.2506077929810.02989661870630.3634301198870.054430207457-0.0550470455440.3605991462610.1305975446850.870394156137-39.346881895583.493725274475.4908088039
202.403668771190.458309970859-0.2793455659412.772672198590.471646241712.30347234052-0.1042190738230.3148739356970.750863665069-0.272875792070.0400245518024-0.438995232111-0.5162928027130.4530301516590.0604415652860.363067808626-0.119848197687-0.05543991823950.4621340021880.2109182850780.734085918846-0.10618926363882.407367764872.0913762978
211.2025750369-0.2781698630540.1607405731670.870297200364-0.2745628396451.328436841480.1743565989060.5910613253240.656136338016-0.503819113101-0.2140731147340.211350077788-0.541209405238-0.2103559056430.006087035280530.5385180842370.000682458449507-0.1079448307390.4505898905140.2962742795760.900171469015-27.317150632987.385998363863.6674450963
221.29397201315-0.6964586431310.3995033874251.83480009958-0.1928795613110.9461004443960.01651287065480.5469744360890.657809732346-0.382877109789-0.001660085989350.119377306801-0.3059998269890.0463115443704-0.004057750243060.398148751631-0.0429957088504-0.02561627585170.4342834446720.3047972241840.737925753295-20.058971491482.32368564264.7229530192
233.286055602320.02899112738170.7360392566971.68440159028-0.6075293743670.431825265631-0.01116378458780.2801464465780.309060039022-0.2632161085120.1183404198690.3069912607840.036681646327-0.105840331421-0.1104231522340.300126340741-0.0315700637493-0.06486790703370.3174281018650.1492024889960.442995154347-29.566575598268.388811919968.2883082561
241.35183969881.12918684345-1.624594352863.03616382314-1.812844010732.87217469427-0.0437003442049-0.02790168063460.1369677181760.02821120578790.0144682860138-0.4523204567260.1140088508110.10199752964-0.04119915473520.259508574523-0.0023570822268-0.06818477820940.3056540796850.1428250324170.631375842776-38.571927440267.777252250876.1366309602
254.052718153283.33184459408-0.07730311729827.30891201878-0.6339118884351.308840296810.227070131173-0.3250265394251.383474842040.942546710863-0.1451044274581.19338831062-0.401755469175-0.461984931611-0.08774745738340.4674814805470.0595767975490.05674702693860.496821176696-0.1202830504310.925067644756-45.022812623986.185127160584.4192759763
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 - 73
22chain 'A' and (resid 81 through 161 )AA81 - 16174 - 154
33chain 'A' and (resid 162 through 271 )AA162 - 271155 - 264
44chain 'A' and (resid 272 through 427 )AA272 - 427265 - 420
55chain 'A' and (resid 428 through 491 )AA428 - 491421 - 484
66chain 'A' and (resid 492 through 600 )AA492 - 528485 - 521
77chain 'B' and (resid 2 through 80 )BG2 - 801 - 73
88chain 'B' and (resid 81 through 161 )BG81 - 16174 - 154
99chain 'B' and (resid 162 through 272 )BG162 - 272155 - 265
1010chain 'B' and (resid 273 through 427 )BG273 - 427266 - 420
1111chain 'B' and (resid 428 through 491 )BG428 - 491421 - 484
1212chain 'B' and (resid 492 through 600 )BG492 - 528485 - 521
1313chain 'C' and (resid 2 through 63 )CN2 - 631 - 56
1414chain 'C' and (resid 64 through 161 )CN64 - 16157 - 154
1515chain 'C' and (resid 162 through 427 )CN162 - 427155 - 420
1616chain 'C' and (resid 428 through 466 )CN428 - 466421 - 459
1717chain 'C' and (resid 467 through 527 )CN467 - 527460 - 520
1818chain 'D' and (resid 2 through 66 )DQ2 - 661 - 59
1919chain 'D' and (resid 67 through 172 )DQ67 - 17260 - 164
2020chain 'D' and (resid 173 through 242 )DQ173 - 242165 - 234
2121chain 'D' and (resid 243 through 272 )DQ243 - 272235 - 264
2222chain 'D' and (resid 273 through 381 )DQ273 - 381265 - 373
2323chain 'D' and (resid 382 through 455 )DQ382 - 455374 - 447
2424chain 'D' and (resid 456 through 491 )DQ456 - 491448 - 483
2525chain 'D' and (resid 492 through 527 )DQ492 - 527484 - 519

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