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- PDB-8ttk: Tryptophan-6-halogenase BorH apo structure -

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Basic information

Entry
Database: PDB / ID: 8ttk
TitleTryptophan-6-halogenase BorH apo structure
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 / Tryptophan 6-halogenase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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

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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)242,34520
Polymers240,8084
Non-polymers1,53716
Water18,5191028
1
A: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7787
Polymers60,2021
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6826
Polymers60,2021
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3943
Polymers60,2021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4904
Polymers60,2021
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.740, 157.580, 112.970
Angle α, β, γ (deg.)90.000, 104.250, 90.000
Int Tables number4
Space group name H-MP1211

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1028 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 53.44 %
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→37.92 Å / Num. obs: 164806 / % possible obs: 95.03 % / Redundancy: 2 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.957 / CC star: 0.989 / Rmerge(I) obs: 0.09669 / Rpim(I) all: 0.09669 / Rrim(I) all: 0.1367 / Net I/σ(I): 5.59
Reflection shellResolution: 1.98→2.051 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 16702 / CC1/2: 0.377 / CC star: 0.74 / Rpim(I) all: 0.753 / Rrim(I) all: 1.065 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→37.92 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1997 1.21 %
Rwork0.221 162865 -
obs0.2214 164625 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.06 Å2 / Biso mean: 39.6448 Å2 / Biso min: 11.03 Å2
Refinement stepCycle: final / Resolution: 1.98→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16646 0 80 1028 17754
Biso mean--52.98 39.09 -
Num. residues----2076
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.030.40911330.3662117451187897
2.03-2.080.39161620.3456117851194797
2.08-2.140.3731440.3102118011194597
2.14-2.210.30861370.2857118221195997
2.21-2.290.34491420.2674117751191796
2.29-2.380.2671350.2492116571179295
2.38-2.490.26161430.2406116931183696
2.49-2.620.27551320.2346108931102589
2.62-2.790.23571330.2185109251105890
2.79-30.251480.2095119861213498
3-3.310.22911520.2048120111216398
3.31-3.780.20261500.1834119311208197
3.78-4.770.18521420.1671114411158393
4.77-37.920.23151440.2066114001154492
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)
12.68471.26271.38522.1826-0.1421.07660.18070.4769-0.1922-0.12350.019-0.62620.3140.5203-0.20160.25170.1290.07190.4153-0.03350.411226.8682126.083572.1601
23.3308-1.0326-0.44431.49320.07351.30230.24550.572-0.5177-0.2455-0.20370.05520.31550.0349-0.02370.33150.0652-0.030.2996-0.12580.2296-0.2445123.450668.2034
35.15140.20120.26574.5681.67440.7890.1388-0.47560.11760.79180.06770.61080.1754-0.2958-0.10930.35260.02680.13170.4053-0.01780.517214.4655137.895977.3705
42.6204-0.12640.27522.78750.56911.06360.158-0.1525-0.28690.2904-0.0635-0.58670.26550.1832-0.12240.28590.0854-0.0170.3258-0.00040.414926.9941127.000280.2583
52.89320.28290.61651.382-0.24551.4943-0.13110.00170.8559-0.00680.08120.1499-0.3338-0.0190.03530.323-0.0501-0.0580.21470.08210.695-18.633785.261577.0497
63.36671.3207-1.51963.7575-0.09011.64250.0845-0.07380.69650.0073-0.07090.474-0.335-0.32-0.03660.234-0.0214-0.05270.35910.11810.7011-47.264475.014475.6168
72.8606-0.19390.55941.4604-0.48591.2298-0.07750.43750.8571-0.240.05740.1361-0.22340.03990.02940.3138-0.0834-0.0810.29780.23360.6151-18.52181.167267.8618
82.91650.4744-0.6142.92631.04071.89320.1374-0.17450.4440.5527-0.007-0.489-0.02130.2912-0.25880.3799-0.0643-0.15840.32960.15120.553-32.880667.121477.4272
92.07071.6484-0.36663.848-1.16190.99220.0405-0.11550.9790.4991-0.06460.7697-0.3222-0.17370.01580.32450.0171-0.06130.34780.03040.7822-45.769377.797379.8623
102.7612-0.68061.77961.3196-0.24382.9149-0.10410.165-0.0887-0.06720.2538-0.42340.19230.5035-0.14360.20380.03880.03650.2632-0.09940.3016-10.8342124.4726124.9012
111.9361-2.0968-0.71762.70540.01121.5402-0.06710.1607-0.0292-0.1580.05310.3133-0.0283-0.17610.00450.1403-0.01960.0030.15230.01550.1659-44.3685129.7655117.0468
121.48650.39840.45951.32160.31411.1432-0.066-0.055-0.23420.1610.152-0.20470.23280.1761-0.08620.21760.06890.04570.1884-0.03550.2564-23.4302116.9348129.5105
131.4664-0.9432-0.84861.87920.51971.8778-0.1216-0.04090.3687-0.00650.1098-0.2607-0.15130.23530.01520.1647-0.0647-0.02790.1677-0.01310.3053-38.2445136.6818121.4746
142.28350.2945-1.25120.69410.41831.7632-0.07580.0690.0829-0.25160.22540.968-0.1273-0.4789-0.11160.23120.025-0.01050.37110.17070.8418-7.799480.5383124.7276
151.1889-1.34530.61261.961-0.53161.7218-0.05010.2460.0189-0.32250.03550.05330.16160.0681-0.02440.2054-0.05-0.01150.1938-0.01840.247423.399675.1066115.285
161.63040.7468-0.43481.8575-0.5851.19380.0535-0.03070.48480.19660.1640.8158-0.3484-0.3042-0.16250.20870.07340.04720.26320.07370.83791.813791.1978127.3867
172.12980.6595-0.61251.1252-0.10060.7910.03-0.12730.43710.21320.03880.5491-0.1208-0.1536-0.05660.21040.02950.01370.2075-0.02260.4468.429884.8088134.4778
183.46780.07650.12491.741-0.54441.22340.0263-0.0394-0.44680.13390.1480.95320.4064-0.48750.11580.2059-0.07620.04720.26130.0440.47116.303568.8379130.8679
193.2988-1.65981.30782.1841-0.90621.61250.02230.2808-0.1465-0.2983-0.00940.3130.1690.11230.00610.1776-0.06750.00220.13340.00030.22822.181368.0215114.8829
206.5224-1.2413-0.16412.5763-0.01721.76730.1436-0.2203-0.63770.1442-0.05390.20490.3779-0.0227-0.0860.2714-0.0369-0.01570.149-0.0030.23-6.1266119.622481.9552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 81 through 151 )C81 - 151
2X-RAY DIFFRACTION2chain 'C' and (resid 152 through 427 )C152 - 427
3X-RAY DIFFRACTION3chain 'C' and (resid 428 through 466 )C428 - 466
4X-RAY DIFFRACTION4chain 'C' and (resid 467 through 527 )C467 - 527
5X-RAY DIFFRACTION5chain 'D' and (resid 2 through 100 )D2 - 100
6X-RAY DIFFRACTION6chain 'D' and (resid 101 through 145 )D101 - 145
7X-RAY DIFFRACTION7chain 'D' and (resid 146 through 427 )D146 - 427
8X-RAY DIFFRACTION8chain 'D' and (resid 428 through 466 )D428 - 466
9X-RAY DIFFRACTION9chain 'D' and (resid 467 through 527 )D467 - 527
10X-RAY DIFFRACTION10chain 'A' and (resid 2 through 80 )A2 - 80
11X-RAY DIFFRACTION11chain 'A' and (resid 81 through 151 )A81 - 151
12X-RAY DIFFRACTION12chain 'A' and (resid 152 through 427 )A152 - 427
13X-RAY DIFFRACTION13chain 'A' and (resid 428 through 527 )A428 - 527
14X-RAY DIFFRACTION14chain 'B' and (resid 2 through 80 )B2 - 80
15X-RAY DIFFRACTION15chain 'B' and (resid 81 through 161 )B81 - 161
16X-RAY DIFFRACTION16chain 'B' and (resid 162 through 315 )B162 - 315
17X-RAY DIFFRACTION17chain 'B' and (resid 316 through 427 )B316 - 427
18X-RAY DIFFRACTION18chain 'B' and (resid 428 through 466 )B428 - 466
19X-RAY DIFFRACTION19chain 'B' and (resid 467 through 527 )B467 - 527
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 80 )C2 - 80

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