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- PDB-8ad7: Flavin-dependent tryptophan 6-halogenase Thal in complex with D-Trp -

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Basic information

Entry
Database: PDB / ID: 8ad7
TitleFlavin-dependent tryptophan 6-halogenase Thal in complex with D-Trp
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / halogenase / ThdH / D-amino acid / D-Trp unnatural substrate / tryptophan halogenase
Function / homology
Function and homology information


tryptophan 6-halogenase / 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
D-TRYPTOPHAN / PHOSPHATE ION / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMoritzer, A.C. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2023
Title: Enzymatic Late-Stage Halogenation of Peptides.
Authors: Schnepel, C. / Moritzer, A.C. / Gafe, S. / Montua, N. / Minges, H. / Niess, A. / Niemann, H.H. / Sewald, N.
History
DepositionJul 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 11, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,59612
Polymers120,5542
Non-polymers1,04210
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric according to gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-18 kcal/mol
Surface area39410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.910, 138.910, 142.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains
21AAA
31BBB

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Components

#1: Protein Tryptophan 6-halogenase


Mass: 60276.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GAMG remain after TEV cleavage of the N-terminal His6-tag
Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal, thdH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-DTR / D-TRYPTOPHAN


Type: D-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.3 Å3/Da / Density % sol: 62.78 % / Description: HEXAGONAL PRISM
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: RESERVOIR: 0.1 M BICINE PH 8.2, 1.6 M K2HPO4/KH2PO4; PROTEIN CONCENTRATION: ~ 15 MG/ML; PROTEIN BUFFER: 10 MM TRIS PH 7.4, 50 MM NACL, 1 MM TCEP; PROTEIN AND SUBSTRATE D-TRP PREINCUBATED ...Details: RESERVOIR: 0.1 M BICINE PH 8.2, 1.6 M K2HPO4/KH2PO4; PROTEIN CONCENTRATION: ~ 15 MG/ML; PROTEIN BUFFER: 10 MM TRIS PH 7.4, 50 MM NACL, 1 MM TCEP; PROTEIN AND SUBSTRATE D-TRP PREINCUBATED BEFORE PLATE SET-UP; DROP RATIO: 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9164 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9164 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 66588 / % possible obs: 100 % / Redundancy: 20.84 % / CC1/2: 0.998 / Rrim(I) all: 0.13 / Net I/σ(I): 14.09
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 21.05 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 4908 / CC1/2: 0.746 / Rrim(I) all: 1.71 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H43 CHAINA

6h43


Resolution: 2.33→49.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.301 / SU ML: 0.188 / Cross valid method: FREE R-VALUE / ESU R: 0.251 / ESU R Free: 0.208
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3342 5.022 %RANDOM
Rwork0.192 ---
obs-66549 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 70.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.337 Å20.168 Å20 Å2
2--0.337 Å20 Å2
3----1.092 Å2
Refinement stepCycle: LAST / Resolution: 2.33→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8401 0 66 224 8691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138686
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177850
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.64511781
X-RAY DIFFRACTIONr_angle_other_deg1.2531.57618158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25151050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45221.667492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.442151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4631564
X-RAY DIFFRACTIONr_chiral_restr0.0680.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021990
X-RAY DIFFRACTIONr_nbd_refined0.2030.21677
X-RAY DIFFRACTIONr_nbd_other0.160.226
X-RAY DIFFRACTIONr_nbtor_refined0.1660.24188
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0857.2754212
X-RAY DIFFRACTIONr_mcbond_other6.0857.2754212
X-RAY DIFFRACTIONr_mcangle_it8.31310.9015258
X-RAY DIFFRACTIONr_mcangle_other8.31210.9015259
X-RAY DIFFRACTIONr_scbond_it6.1637.7374474
X-RAY DIFFRACTIONr_scbond_other6.1627.7374474
X-RAY DIFFRACTIONr_scangle_it8.62411.4016523
X-RAY DIFFRACTIONr_scangle_other8.62311.46524
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.39 Å
RfactorNum. reflection% reflection
Rfree0.36 250 -
Rwork0.314 4649 -
obs--99.69 %

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