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- PDB-6h44: Flavin-dependent Tryptophan 6-halogenase Thal in complex with try... -

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Basic information

Entry
Database: PDB / ID: 6h44
TitleFlavin-dependent Tryptophan 6-halogenase Thal in complex with tryptophan
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / tryptophan halogenase / ThdH / substrate-bound
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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / TRYPTOPHAN / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMoritzer, A. / Minges, H. / Sewald, N. / Niemann, H.H.
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structure-based switch of regioselectivity in the flavin-dependent tryptophan 6-halogenase Thal.
Authors: Moritzer, A.C. / Minges, H. / Prior, T. / Frese, M. / Sewald, N. / Niemann, H.H.
History
DepositionJul 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)122,95626
Polymers120,5542
Non-polymers2,40224
Water3,549197
1
A: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,63415
Polymers60,2771
Non-polymers1,35714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,32211
Polymers60,2771
Non-polymers1,04510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.700, 136.700, 144.900
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

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Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan 6-halogenase


Mass: 60276.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal, thdH / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280

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Non-polymers , 5 types, 221 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
23.2662.26hexagonal prism
1
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M bicine pH 9.0, 1.6 M K2HPO4/NaH2PO4 protein concentration: ~15 mg/mL protein buffer:10 mM Tris pH 7.4, 50 mM NaCl and 1 mM TCEP drop ratio: 1:1 (P:R)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 50056 / % possible obs: 100 % / Redundancy: 20.59 % / Biso Wilson estimate: 52.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.172 / Net I/σ(I): 15.89
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 20.74 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 3700 / CC1/2: 0.666 / Rrim(I) all: 1.776 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Thal

Resolution: 2.55→49.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.354 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22506 2462 4.9 %RANDOM
Rwork0.17892 ---
obs0.18118 47558 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.55→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8432 0 150 197 8779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0148838
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177699
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.66711986
X-RAY DIFFRACTIONr_angle_other_deg0.8751.6518025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79151064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63821.657501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.009151395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3761565
X-RAY DIFFRACTIONr_chiral_restr0.0610.21117
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021763
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_it4.3595.5894253
X-RAY DIFFRACTIONr_mcbond_other4.3595.5894252
X-RAY DIFFRACTIONr_mcangle_it6.3568.3895318
X-RAY DIFFRACTIONr_mcangle_other6.3558.3895319
X-RAY DIFFRACTIONr_scbond_it4.815.9814585
X-RAY DIFFRACTIONr_scbond_other4.815.9814585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.068.7976669
X-RAY DIFFRACTIONr_long_range_B_refined8.90763.7339756
X-RAY DIFFRACTIONr_long_range_B_other8.90663.7149720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17997 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 190 -
Rwork0.298 3494 -
obs--99.92 %

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