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- PDB-6ib5: Mutant of flavin-dependent tryptophan halogenase Thal with altere... -

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Basic information

Entry
Database: PDB / ID: 6ib5
TitleMutant of flavin-dependent tryptophan halogenase Thal with altered regioselectivity (Thal-RebH5)
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / tryptophan halogenase / ThdH / Thal
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: 2.12 Å
AuthorsMoritzer, A. / Prior, T. / 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
DepositionNov 29, 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 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan 6-halogenase
B: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,14517
Polymers120,7522
Non-polymers1,39315
Water7,566420
1
A: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0248
Polymers60,3761
Non-polymers6487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan 6-halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1229
Polymers60,3761
Non-polymers7458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.260, 139.260, 144.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Tryptophan 6-halogenase


Mass: 60376.117 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
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.35 Å3/Da / Density % sol: 63.3 % / Description: hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.1 M bicine pH 8.4, 1.3 M K2HPO4/KH2PO4 protein concentration: ~15 mg/mL protein buffer: 10 mM Tris pH 7.4, 50 mM NaCl and 1 mM TCEP drop ratio: 2:1 (P:R)

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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: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 89845 / % possible obs: 100 % / Redundancy: 17.89 % / Biso Wilson estimate: 59.845 Å2 / CC1/2: 1 / Rrim(I) all: 0.076 / Net I/σ(I): 20.74
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 18.66 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 6649 / CC1/2: 0.763 / Rrim(I) all: 1.857 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3199: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H44

6h44


Resolution: 2.12→48.11 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.29
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 4494 5.01 %RANDOM
Rwork0.1632 ---
obs0.1646 89790 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8395 0 86 420 8901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078763
X-RAY DIFFRACTIONf_angle_d0.86611889
X-RAY DIFFRACTIONf_dihedral_angle_d14.215172
X-RAY DIFFRACTIONf_chiral_restr0.0541258
X-RAY DIFFRACTIONf_plane_restr0.0061546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.14410.31511500.2752869X-RAY DIFFRACTION100
2.1441-2.16930.30961510.26182784X-RAY DIFFRACTION100
2.1693-2.19580.34661510.25052884X-RAY DIFFRACTION100
2.1958-2.22360.25871490.23722799X-RAY DIFFRACTION100
2.2236-2.25280.26691380.22252865X-RAY DIFFRACTION100
2.2528-2.28370.23041380.22012863X-RAY DIFFRACTION100
2.2837-2.31630.2441590.2142787X-RAY DIFFRACTION100
2.3163-2.35090.25141540.21822818X-RAY DIFFRACTION100
2.3509-2.38760.26541460.19942849X-RAY DIFFRACTION100
2.3876-2.42680.26771680.19822807X-RAY DIFFRACTION100
2.4268-2.46860.231500.1942843X-RAY DIFFRACTION100
2.4686-2.51350.19771650.18922811X-RAY DIFFRACTION100
2.5135-2.56190.25371740.18212822X-RAY DIFFRACTION100
2.5619-2.61410.24911430.19512858X-RAY DIFFRACTION100
2.6141-2.6710.2651610.19612839X-RAY DIFFRACTION100
2.671-2.73310.23661610.18712812X-RAY DIFFRACTION100
2.7331-2.80150.23231450.18542834X-RAY DIFFRACTION100
2.8015-2.87720.22661430.18032837X-RAY DIFFRACTION100
2.8772-2.96180.23171360.19292879X-RAY DIFFRACTION100
2.9618-3.05740.24161500.18952827X-RAY DIFFRACTION100
3.0574-3.16670.22971510.18932847X-RAY DIFFRACTION100
3.1667-3.29340.19491510.18042835X-RAY DIFFRACTION100
3.2934-3.44330.21161370.16892876X-RAY DIFFRACTION100
3.4433-3.62480.19021610.15512809X-RAY DIFFRACTION100
3.6248-3.85180.16461360.15152873X-RAY DIFFRACTION100
3.8518-4.1490.15321610.13862838X-RAY DIFFRACTION100
4.149-4.56630.15371520.12332846X-RAY DIFFRACTION100
4.5663-5.22630.13311270.1272891X-RAY DIFFRACTION100
5.2263-6.5820.17421420.15512882X-RAY DIFFRACTION100
6.582-48.12240.16431440.15052912X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.927 Å / Origin y: -64.2287 Å / Origin z: -25.9241 Å
111213212223313233
T0.3653 Å20.0195 Å20.0628 Å2-0.4227 Å20.0207 Å2--0.3515 Å2
L1.4369 °20.4745 °2-0.6329 °2-0.627 °2-0.5113 °2--1.0813 °2
S-0.1648 Å °0.0267 Å °-0.2345 Å °-0.1058 Å °0.0661 Å °-0.1033 Å °0.1359 Å °-0.0084 Å °0.0357 Å °
Refinement TLS groupSelection details: all

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