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- PDB-8fov: AbeH (Tryptophan-5-halogenase) bound to FAD and Cl -

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Basic information

Entry
Database: PDB / ID: 8fov
TitleAbeH (Tryptophan-5-halogenase) bound to FAD and Cl
ComponentsTryptophan 5-halogenase
KeywordsOXIDOREDUCTASE / halogenase / flavin
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 superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 5-halogenase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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
Citation
Journal: Acs Omega / Year: 2025
Title: Crystallographic and Thermodynamic Evidence of Negative Coupling in the Flavin-Dependent Tryptophan Halogenases AbeH and BorH.
Authors: Ashaduzzaman, M. / Lingkon, K. / De Silva, A.J. / Bellizzi 3rd, J.J.
#1: Journal: 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
Revision 1.2Jul 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,31618
Polymers116,7012
Non-polymers2,61516
Water14,574809
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A: Tryptophan 5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6589
Polymers58,3511
Non-polymers1,3078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan 5-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6589
Polymers58,3511
Non-polymers1,3078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.710, 112.290, 173.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan 5-halogenase


Mass: 58350.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Contains extra Proline at N-terminus (residue 0) remaining from cleavage of linker with N-terminal His-tag.
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: abeH / Production host: Escherichia coli (E. coli) / References: UniProt: F6LWA5

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Non-polymers , 5 types, 825 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Drop:1:1 ratio of reservoir solution and (50uM AbeH/25 mM FAD in 20 mM HEPES pH 7.2 and 35 mM sodium citrate); Reservoir (500 uL): 0.1 M Bis-Tris pH 6.2, 0.2 M magnesium acetate, 11% (v/v) PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.86→56.14 Å / Num. obs: 93637 / % possible obs: 99.63 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.06443 / Rpim(I) all: 0.06443 / Rrim(I) all: 0.09112 / Net I/σ(I): 7.1
Reflection shellResolution: 1.86→1.926 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3797 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 9276 / CC1/2: 0.708 / CC star: 0.911 / Rpim(I) all: 0.3797 / Rrim(I) all: 0.537 / % possible all: 99.96

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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: 1.86→56.14 Å / SU ML: 0.1911 / Cross valid method: FREE R-VALUE / σ(F): 0.6 / Phase error: 20.1232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1943 894 0.95 %
Rwork0.1658 92730 -
obs0.1661 93623 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.53 Å2
Refinement stepCycle: LAST / Resolution: 1.86→56.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7954 0 172 809 8935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00398376
X-RAY DIFFRACTIONf_angle_d0.63811391
X-RAY DIFFRACTIONf_chiral_restr0.04481188
X-RAY DIFFRACTIONf_plane_restr0.00531471
X-RAY DIFFRACTIONf_dihedral_angle_d13.13052968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.980.23721480.232215294X-RAY DIFFRACTION99.97
1.98-2.130.23131480.193715354X-RAY DIFFRACTION99.98
2.13-2.340.22151480.174315385X-RAY DIFFRACTION99.97
2.34-2.680.19541490.166415440X-RAY DIFFRACTION99.94
2.68-3.380.17141490.159515481X-RAY DIFFRACTION99.66
3.38-56.140.18421520.149215776X-RAY DIFFRACTION98.34

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