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- PDB-6ul2: Crystal structure of tryptophan-6-halogenase BorH complexed with ... -

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Basic information

Entry
Database: PDB / ID: 6ul2
TitleCrystal structure of tryptophan-6-halogenase BorH complexed with L-tryptophan
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / halogenase oxidoreductase
Function / homology
Function and homology information


monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHAN / Tryptophan 6-halogenase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsLingkon, K. / Bellizzi, J.J.
CitationJournal: Chembiochem / Year: 2020
Title: Structure and Activity of the Thermophilic Tryptophan-6 Halogenase BorH.
Authors: Lingkon, K. / Bellizzi 3rd, J.J.
History
DepositionOct 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)244,21935
Polymers240,8084
Non-polymers3,41131
Water22,9871276
1
A: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,17510
Polymers60,2021
Non-polymers9739
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,17510
Polymers60,2021
Non-polymers9739
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
4
D: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9838
Polymers60,2021
Non-polymers7817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.480, 157.920, 113.250
Angle α, β, γ (deg.)90.000, 104.060, 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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1276 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
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: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.979→32.06 Å / Num. obs: 170635 / % possible obs: 98.2 % / Redundancy: 4.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.082 / Rrim(I) all: 0.182 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.98-2.014.90.7984145384450.6770.3990.8952.299.2
10.84-32.064.70.114486910300.9790.0580.12910.394.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.7.3data scaling
MOSFLMdata reduction
PHASERphasing
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OAM
Resolution: 1.979→31.8942 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 22.82
RfactorNum. reflection% reflection
Rfree0.2288 2000 1.17 %
Rwork0.1929 --
obs0.1933 170571 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.77 Å2 / Biso mean: 35.3735 Å2 / Biso min: 5.05 Å2
Refinement stepCycle: final / Resolution: 1.979→31.8942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16681 0 195 1276 18152
Biso mean--49.2 35.24 -
Num. residues----2081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617339
X-RAY DIFFRACTIONf_angle_d0.88123571
X-RAY DIFFRACTIONf_chiral_restr0.0372445
X-RAY DIFFRACTIONf_plane_restr0.0043083
X-RAY DIFFRACTIONf_dihedral_angle_d12.1736223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.979-2.02850.28921500.25751209499
2.0285-2.08330.28321430.24161211499
2.0833-2.14460.26051470.22061209399
2.1446-2.21380.24321370.21191214399
2.2138-2.29290.23961530.20011210799
2.2929-2.38470.27991390.20241208699
2.3847-2.49320.25121430.20611204799
2.4932-2.62460.28191360.20851172395
2.6246-2.78890.23481440.2011163595
2.7889-3.00410.23361440.20041212199
3.0041-3.30610.22741460.19731219099
3.3061-3.78390.20731460.17941219499
3.7839-4.76470.20961340.16081206998
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)
13.1267-0.80212.25980.8947-0.57173.6278-0.00440.1751-0.011-0.11810.1857-0.29720.16760.3355-0.15330.1772-0.00750.06130.2347-0.10710.2846-10.6728123.4308125.7799
20.6832-1.15210.09412.1790.21821.2073-0.11730.17420.0755-0.140.01780.2123-0.0931-0.05060.07150.158-0.0494-0.01010.16730.01620.1914-41.4535130.2729116.0723
31.53510.34540.58021.05310.32690.9578-0.06630.0253-0.20170.10520.1931-0.14860.12360.1495-0.07890.18140.04370.03860.1593-0.04550.2413-22.949116.4712131.0363
41.434-0.7464-0.26191.22010.70881.097-0.08160.11170.2522-0.13660.0351-0.0603-0.170.01640.04050.1958-0.052-0.02230.13620.0380.2665-37.5538137.0537122.1733
52.70680.0435-1.66861.02180.27051.2335-0.1070.3310.24-0.20430.35590.83730.0059-0.401-0.15740.2095-0.0233-0.05160.33850.18960.6953-8.084180.8961125.1028
60.6634-0.61540.12081.8277-0.42011.2965-0.02270.14350.0388-0.27510.00470.03560.18570.04380.01060.1807-0.05240.0030.1778-0.00440.171423.00575.2105115.5328
71.27591.0393-0.51811.6787-0.6390.96080.05480.04760.47210.13990.17530.6464-0.161-0.167-0.11750.17320.03280.03650.18250.04130.52124.563988.7905130.7201
81.0929-0.3350.16561.309-0.6021.1325-0.08180.089-0.1798-0.21940.12210.23150.2128-0.0697-0.03730.2-0.0682-0.00730.1456-0.00350.259319.122968.4201121.4434
94.0055-1.17720.20173.44720.39511.78910.0427-0.1127-0.49030.0292-0.03590.2430.261-0.15790.02970.2308-0.02490.03090.1392-0.00450.2728-8.8977122.458882.4377
102.1059-0.51730.21692.01230.35121.52910.07410.0831-0.3424-0.14190.0304-0.11110.19360.1704-0.08770.2730.1085-0.00770.1922-0.0350.339818.304120.684274.514
114.33330.9055-0.41351.39790.08510.67940.10260.0292-0.50320.12520.0035-0.02760.23790.0692-0.09160.28960.0733-0.02470.2095-0.02830.283616.7085120.268380.6642
121.9984-1.1025-0.38211.23310.24681.02720.23960.3898-0.4801-0.1672-0.23270.3050.2137-0.17180.02640.29470.0406-0.04670.2626-0.11370.3237-10.1288123.009468.7142
131.68390.58720.38331.03640.27852.19270.53880.3493-1.3137-0.6413-0.3548-0.05120.497-0.28830.20350.58670.366-0.01290.3232-0.41760.17311.2736116.200558.8386
142.1123-0.9381-0.60771.26640.42961.55530.19670.3925-0.1293-0.2164-0.16830.00920.10530.0966-0.00690.22610.06760.00020.2385-0.04950.2271.6762130.679868.0608
152.20190.0912-0.122.21390.05610.85110.0524-0.0806-0.02610.17660.0168-0.26820.12050.115-0.06710.2440.06690.03530.2236-0.05250.328221.9983131.656880.2406
162.2914-0.0685-0.22222.3634-0.49470.9408-0.1621-0.18850.55720.04990.0678-0.1408-0.26430.05660.060.2842-0.0451-0.09060.18830.00670.6107-8.678282.41181.7357
170.74160.2123-0.43151.6959-0.25820.898-0.1616-0.04041.15730.01140.09420.4331-0.2627-0.29950.01190.33740.0303-0.16760.17730.18740.8852-36.220684.47573.1076
181.6351.30140.33561.13560.43070.4931-0.1141-0.27530.6306-0.0636-0.00940.111-0.2527-0.15190.06890.30940.0128-0.10190.24790.09670.8239-35.207684.695479.2371
190.3514-0.13150.34740.9827-0.28930.7807-0.16090.49430.8653-0.18920.001-0.0575-0.23230.24480.07850.3294-0.0923-0.10430.33160.20020.7286-7.906281.730267.5658
201.5999-0.41320.06340.8891-0.13530.6776-0.00720.53820.6352-0.27330.02770.0958-0.15430.18190.10630.3241-0.0926-0.10340.25860.26890.6004-20.454179.286665.6396
211.56570.52010.10691.9393-0.49470.8482-0.07440.01130.50160.04430.10040.2453-0.1147-0.1247-0.03950.23940.0072-0.10270.2230.07720.5055-39.164573.313175.2544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 80 )A2 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 161 )A81 - 161
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 427 )A162 - 427
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 527 )A428 - 527
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 80 )B2 - 80
6X-RAY DIFFRACTION6chain 'B' and (resid 81 through 161 )B81 - 161
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 427 )B162 - 427
8X-RAY DIFFRACTION8chain 'B' and (resid 428 through 527 )B428 - 527
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 63 )C3 - 63
10X-RAY DIFFRACTION10chain 'C' and (resid 64 through 121 )C64 - 121
11X-RAY DIFFRACTION11chain 'C' and (resid 122 through 187 )C122 - 187
12X-RAY DIFFRACTION12chain 'C' and (resid 188 through 272 )C188 - 272
13X-RAY DIFFRACTION13chain 'C' and (resid 273 through 315 )C273 - 315
14X-RAY DIFFRACTION14chain 'C' and (resid 316 through 427 )C316 - 427
15X-RAY DIFFRACTION15chain 'C' and (resid 428 through 527 )C428 - 527
16X-RAY DIFFRACTION16chain 'D' and (resid 3 through 63 )D3 - 63
17X-RAY DIFFRACTION17chain 'D' and (resid 64 through 121 )D64 - 121
18X-RAY DIFFRACTION18chain 'D' and (resid 122 through 187 )D122 - 187
19X-RAY DIFFRACTION19chain 'D' and (resid 188 through 272 )D188 - 272
20X-RAY DIFFRACTION20chain 'D' and (resid 273 through 409 )D273 - 409
21X-RAY DIFFRACTION21chain 'D' and (resid 410 through 527 )D410 - 527

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