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- PDB-8fox: AbeH (Tryptophan-5-halogenase) -

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Basic information

Entry
Database: PDB / ID: 8fox
TitleAbeH (Tryptophan-5-halogenase)
ComponentsTryptophan 5-halogenase
KeywordsOXIDOREDUCTASE / halogenase / flavin
Function / homologyFlavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / nucleotide binding / Tryptophan 5-halogenase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsAshaduzzaman, M. / 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
DepositionJan 3, 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan 5-halogenase
B: Tryptophan 5-halogenase
C: Tryptophan 5-halogenase
D: Tryptophan 5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,55516
Polymers233,4024
Non-polymers1,15312
Water36,0662002
1
A: Tryptophan 5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7355
Polymers58,3511
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan 5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6394
Polymers58,3511
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tryptophan 5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5433
Polymers58,3511
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tryptophan 5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6394
Polymers58,3511
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.450, 251.130, 68.010
Angle α, β, γ (deg.)90.000, 108.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tryptophan 5-halogenase


Mass: 58350.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: abeH / Production host: Escherichia coli (E. coli) / References: UniProt: F6LWA5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2002 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Drop: 2 uL of 40 uM AbeH/20 mM HEPES pH 7.5/350 mM NaCl + 2 uL of reservoir solution Reservoir solution: 500 uL of 100 mM Bis-Tris Propane pH 7.0, 150 mM MgSO4, 25% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.89→60.1 Å / Num. obs: 159987 / % possible obs: 99.88 % / Observed criterion σ(I): 2.88 / Redundancy: 2 % / Biso Wilson estimate: 18.52 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.04645 / Rpim(I) all: 0.04645 / Rrim(I) all: 0.06569 / Net I/σ(I): 9.27
Reflection shellResolution: 1.89→1.958 Å / Redundancy: 2 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 15847 / CC1/2: 0.8 / CC star: 0.943 / Rpim(I) all: 0.274 / Rrim(I) all: 0.3875 / % possible all: 99.37

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→60.1 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 2008 1.25 %
Rwork0.1575 158376 -
obs0.1578 159987 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.19 Å2 / Biso mean: 23.34 Å2 / Biso min: 7.42 Å2
Refinement stepCycle: final / Resolution: 1.89→60.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15684 0 60 2002 17746
Biso mean--37 33.69 -
Num. residues----1963
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 (%)
1.89-1.940.28951550.2317111421129799
1.94-1.990.2361410.19421130811449100
1.99-2.050.19511280.1761134811476100
2.05-2.110.19991540.16481130111455100
2.11-2.190.23011410.16241136111502100
2.19-2.280.20461440.16131129611440100
2.28-2.380.21831460.16271126311409100
2.38-2.50.18551350.15241133411469100
2.5-2.660.20121490.1581130411453100
2.66-2.870.18351450.16061134911494100
2.87-3.150.18481330.15431131511448100
3.16-3.610.15581480.14261135011498100
3.61-4.550.14631440.13321138311527100
4.55-60.10.17271450.1615113221146799
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)
12.20340.83610.26611.4428-0.14450.72070.0675-0.10750.0810.1261-0.0232-0.0557-0.11250.0013-0.04430.11760.00240.01940.0897-0.00260.090922.795214.32353.595
20.63250.1806-0.52293.2076-2.13413.18570.0876-0.1071-0.20980.01060.17230.41240.1083-0.3533-0.2090.1152-0.0120.01860.170.05230.22133.421192.64961.508
31.91570.0078-0.52041.3016-0.1810.87740.00580.04310.1146-0.0614-0.0065-0.1543-0.10180.0668-0.01930.1183-0.02350.00020.098-0.00460.088127.866215.82849.011
41.03360.13880.04381.9971-0.5062.62430.14220.19840.0268-0.3737-0.03340.1187-0.1542-0.1189-0.06320.1462-0.0667-0.01370.11390.00850.095314.703205.38940.445
50.63030.0470.1010.9999-0.13280.64440.03270.0301-0.0554-0.13140.009-0.00570.03890.0111-0.03690.1005-0.00910.00710.0936-0.00430.08119.385198.44646.702
61.54450.5117-0.77023.0052-1.42351.6590.0277-0.15790.07820.58080.23580.6899-0.3723-0.308-0.22250.15640.05630.10970.28460.02120.2888-0.456209.63565.617
70.6060.3118-0.13611.3275-0.28411.149-0.01680.0195-0.0775-0.10180.0509-0.13260.01490.04920.00170.08130.00460.00540.0936-0.01840.1191-22.741117.57835.379
81.18350.1362-0.73461.05380.10351.5493-0.012-0.0154-0.15540.0326-0.0110.00670.1493-0.06960.04120.0924-0.0021-0.03050.08580.01650.1264-33.15108.11342.885
91.63730.08210.95832.81350.16060.75820.08040.2403-0.2185-0.3774-0.02860.041-0.0012-0.026-0.04110.1524-0.0272-0.02540.12850.04290.0935-34.57117.95725.669
100.43220.15050.16680.95460.11140.7022-0.02360.0308-0.0429-0.13580.0425-0.0157-0.0560.0077-0.01250.0874-0.00650.00250.09470.00720.1046-29.263124.70433.092
112.06910.94760.48582.91510.09722.02060.0912-0.1062-0.02930.13920.05630.0619-0.0931-0.1069-0.1330.1517-0.03620.03150.15260.05230.119516.532173.28482.037
121.22170.37230.57361.6787-0.43811.05910.0115-0.09260.13130.2534-0.0561-0.0145-0.14950.02320.01380.1979-0.0048-0.02250.1221-0.01240.103733.356192.02384.932
130.58430.19440.15731.0241-0.10750.81910.0521-0.086-0.03480.0973-0.02160.03980.055-0.032-0.01920.0987-0.001-0.00340.13180.02830.117925.326178.88581.798
142.1496-0.36050.29431.6968-0.23911.1684-0.062-0.2187-0.26150.3598-0.0069-0.22670.21450.19410.05110.2104-0.0038-0.01680.16640.08130.212842.583174.59886.867
150.79770.45260.27371.1819-0.3290.754-0.02380.0912-0.007-0.0868-0.0219-0.11260.01390.14180.02770.0988-0.01340.01740.1310.00960.120434.278183.68269.154
163.20132.6587-2.75164.6827-3.19416.67560.3805-0.41180.25450.7357-0.1424-0.0309-0.56740.329-0.17330.2542-0.0191-0.05210.1742-0.04430.227532.538205.01291.435
170.84960.13820.11362.0003-0.6471.7504-0.07280.10930.0157-0.0870.0175-0.2307-0.24370.29590.05980.1551-0.0693-0.00110.16520.0150.12980.803150.55148.489
181.02640.34080.1861.73050.14670.96840.0703-0.1353-0.13820.1445-0.0487-0.08450.1160.0526-0.00910.1441-0.0094-0.03520.1260.02210.1107-5.854126.2465.442
191.12160.04070.40351.72-0.39550.8822-0.14070.06110.2698-0.039-0.0409-0.0732-0.42580.12140.15140.2938-0.0636-0.03530.15490.01540.1449-4.373161.95549.007
201.1767-0.28210.39851.62080.14721.46170.0153-0.18830.2640.3474-0.0909-0.1242-0.2150.04120.06330.2825-0.07260.00510.1479-0.00890.1396-7.123149.81273.201
210.57660.41610.13041.2803-0.29390.7890.037-0.09260.04450.0944-0.01810.1778-0.0878-0.0871-0.03530.1031-0.00260.0250.1116-0.0080.1063-19.406140.54858.027
224.85581.86930.3153.6037-0.1611.658-0.0264-0.132-0.34470.2686-0.0137-0.62660.06830.2476-0.00630.19260.0301-0.06980.15960.0140.1822.842120.02164.569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:88 )A0 - 88
2X-RAY DIFFRACTION2( CHAIN A AND RESID 89:124 )A89 - 124
3X-RAY DIFFRACTION3( CHAIN A AND RESID 125:240 )A125 - 240
4X-RAY DIFFRACTION4( CHAIN A AND RESID 241:270 )A241 - 270
5X-RAY DIFFRACTION5( CHAIN A AND RESID 271:480 )A271 - 480
6X-RAY DIFFRACTION6( CHAIN A AND RESID 481:514 )A481 - 514
7X-RAY DIFFRACTION7( CHAIN B AND RESID 0:124 )B0 - 124
8X-RAY DIFFRACTION8( CHAIN B AND RESID 125:240 )B125 - 240
9X-RAY DIFFRACTION9( CHAIN B AND RESID 241:270 )B241 - 270
10X-RAY DIFFRACTION10( CHAIN B AND RESID 271:514 )B271 - 514
11X-RAY DIFFRACTION11( CHAIN C AND RESID 0:58 )C0 - 58
12X-RAY DIFFRACTION12( CHAIN C AND RESID 59:104 )C59 - 104
13X-RAY DIFFRACTION13( CHAIN C AND RESID 105:240 )C105 - 240
14X-RAY DIFFRACTION14( CHAIN C AND RESID 241:333 )C241 - 333
15X-RAY DIFFRACTION15( CHAIN C AND RESID 334:480 )C334 - 480
16X-RAY DIFFRACTION16( CHAIN C AND RESID 481:510 )C481 - 510
17X-RAY DIFFRACTION17( CHAIN D AND RESID 0:70 )D0 - 70
18X-RAY DIFFRACTION18( CHAIN D AND RESID 71:166 )D71 - 166
19X-RAY DIFFRACTION19( CHAIN D AND RESID 167:240 )D167 - 240
20X-RAY DIFFRACTION20( CHAIN D AND RESID 241:333 )D241 - 333
21X-RAY DIFFRACTION21( CHAIN D AND RESID 334:480 )D334 - 480
22X-RAY DIFFRACTION22( CHAIN D AND RESID 481:509 )D481 - 509

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