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- PDB-6h43: Flavin-dependent Tryptophan 6-halogenase Thal -

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Basic information

Entry
Database: PDB / ID: 6h43
TitleFlavin-dependent Tryptophan 6-halogenase Thal
ComponentsTryptophan 6-halogenase Thal
KeywordsFLAVOPROTEIN / tryptophan halogenase / ThdH
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 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMoritzer, A. / Minges, H. / Frese, M. / 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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 Thal
B: Tryptophan 6-halogenase Thal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,36022
Polymers120,5542
Non-polymers1,80620
Water5,747319
1
A: Tryptophan 6-halogenase Thal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,33513
Polymers60,2771
Non-polymers1,05812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tryptophan 6-halogenase Thal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0259
Polymers60,2771
Non-polymers7488
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.470, 139.470, 142.510
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 Thal


Mass: 60276.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 319 / 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

CrystalDensity Matthews: 3.25 Å3/Da / Density meas: 0.13 Mg/m3 / Density % sol: 62.2 % / Description: hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: reservoir: 0.1 M Tris pH 8.5, 1.5 M K2HPO4/KH2PO4 protein concentration: ~ 15mg/mL drop ratio: 2:1 (P:R) protein buffer: 10 mM Tris pH 7.4, 50 mM NaCl and 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→49.89 Å / Num. obs: 79654 / % possible obs: 100 % / Redundancy: 8.5 % / Biso Wilson estimate: 52.9 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.14 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5887 / CC1/2: 0.634 / Rrim(I) all: 1.841 / % 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: 2OAM, 2AQJ, 2WEU, 5HY5

2oam

2aqj

2weu

5hy5


Resolution: 2.2→49.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.531 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 3990 5 %RANDOM
Rwork0.16966 ---
obs0.17168 75624 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å2-0 Å2
3----1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8376 0 109 319 8804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0148750
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177639
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.66511867
X-RAY DIFFRACTIONr_angle_other_deg0.9311.64817891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70651059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17921.67497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.117151390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.721565
X-RAY DIFFRACTIONr_chiral_restr0.0750.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021736
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_it4.1174.7174221
X-RAY DIFFRACTIONr_mcbond_other4.1184.7164220
X-RAY DIFFRACTIONr_mcangle_it5.7147.0585279
X-RAY DIFFRACTIONr_mcangle_other5.7147.0595280
X-RAY DIFFRACTIONr_scbond_it5.1845.2634529
X-RAY DIFFRACTIONr_scbond_other5.1825.2644529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4037.6686587
X-RAY DIFFRACTIONr_long_range_B_refined9.12153.9389454
X-RAY DIFFRACTIONr_long_range_B_other9.12453.9439455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16867 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 288 -
Rwork0.298 5594 -
obs--99.95 %

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