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- PDB-8ad8: Flavin-dependent tryptophan 6-halogenase Thal in complex with a D... -

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Basic information

Entry
Database: PDB / ID: 8ad8
TitleFlavin-dependent tryptophan 6-halogenase Thal in complex with a D-Trp-Ser dipeptide
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / halogenase / ThdH / dipeptide / 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-tryptophyl-L-serine / PHOSPHATE ION / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGafe, S. / Moritzer, A.C. / Montua, N. / Sewald, N. / 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 1.4Jun 14, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)121,1246
Polymers120,5542
Non-polymers5704
Water1086
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 area4610 Å2
ΔGint-14 kcal/mol
Surface area38820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.200, 137.200, 143.800
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
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 2 - 529 / Label seq-ID: 5 - 532

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-LT0 / D-tryptophyl-L-serine / (2~{S})-2-[[(2~{R})-2-azanyl-3-(1~{H}-indol-3-yl)propanoyl]amino]-3-oxidanyl-propanoic acid / D-Trp-Ser dipeptide


Type: peptide linking / Mass: 291.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.25 Å3/Da / Density % sol: 62.16 % / Description: hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Reservoir solution: 100 mM Bicine pH 9.0, 1.6 M KH2PO4/K2HPO4; Protein concentration: 15 mg/ml; Protein buffer: 10 mM Tris pH 7.4, 50 mM NaCl, 1 mM DTT; Drop ratio: 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.95→47.98 Å / Num. obs: 32396 / % possible obs: 100 % / Redundancy: 10.54 % / Biso Wilson estimate: 69 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.154 / Net I/σ(I): 16.71
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 11.03 % / Mean I/σ(I) obs: 1.99 / Num. unique obs: 2386 / CC1/2: 0.676 / Rrim(I) all: 1.54 / % 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

6h43


Resolution: 2.95→47.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.589 / SU ML: 0.329 / Cross valid method: FREE R-VALUE / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24988 1577 4.9 %RANDOM
Rwork0.19244 ---
obs0.19528 30787 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.62 Å20 Å2
2--1.23 Å20 Å2
3----4 Å2
Refinement stepCycle: 1 / Resolution: 2.95→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8297 0 38 6 8341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138561
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177742
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.64611614
X-RAY DIFFRACTIONr_angle_other_deg1.2171.57817907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.551036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40121.704487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.326151371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1881563
X-RAY DIFFRACTIONr_chiral_restr0.0640.21081
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021966
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it6.1377.4164156
X-RAY DIFFRACTIONr_mcbond_other6.1357.4144154
X-RAY DIFFRACTIONr_mcangle_it9.10611.1135188
X-RAY DIFFRACTIONr_mcangle_other9.10411.1135188
X-RAY DIFFRACTIONr_scbond_it5.9477.7914405
X-RAY DIFFRACTIONr_scbond_other5.947.7914402
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9511.5156421
X-RAY DIFFRACTIONr_long_range_B_refined11.79284.0439355
X-RAY DIFFRACTIONr_long_range_B_other11.79284.0469356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17045 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 119 -
Rwork0.326 2263 -
obs--99.67 %

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