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- PDB-7aqv: Flavin-dependent tryptophan halogenase Thal: N-terminally His-tag... -

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Basic information

Entry
Database: PDB / ID: 7aqv
TitleFlavin-dependent tryptophan halogenase Thal: N-terminally His-tagged form of quintuple mutant (NHis-Thal-RebH5)
ComponentsTryptophan 6-halogenase
KeywordsFLAVOPROTEIN / tryptophan halogenase / ThdH / His-Tag
Function / homologytryptophan 6-halogenase / Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / nucleotide binding / Tryptophan 6-halogenase ThaL
Function and homology information
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMoritzer, A.C. / Prior, T. / Niemann, H.H.
CitationJournal: Crystals / Year: 2020
Title: Not Cleaving the His-tag of Thal Results in More Tightly Packed and Better-Diffracting Crystals
Authors: Moritzer, A.C. / Prior, T. / Niemann, H.H.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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)124,9094
Polymers124,7252
Non-polymers1842
Water14,412800
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-12 kcal/mol
Surface area40190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.000, 119.110, 87.330
Angle α, β, γ (deg.)90.000, 104.825, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 73 or resid 75...
d_2ens_1(chain "B" and (resid 0 through 42 or resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISGLUA1 - 71
d_12ens_1ASNGLYA73 - 101
d_13ens_1THRPROA103 - 114
d_14ens_1ALATHRA116 - 134
d_15ens_1GLUMETA136 - 160
d_16ens_1ALAGLUA163 - 195
d_17ens_1THRLEUA197 - 218
d_18ens_1GLYASPA220 - 221
d_19ens_1PHEALAA223 - 237
d_110ens_1GLUALAA239 - 276
d_111ens_1GLUASPA278 - 380
d_112ens_1VALASPA382 - 396
d_113ens_1THRALAA398 - 451
d_114ens_1PHEARGA453 - 454
d_115ens_1PHEGLYA456 - 520
d_116ens_1GOLGOLB
d_21ens_1HISILEC6 - 48
d_22ens_1GLYGLUC52 - 79
d_23ens_1ASNGLYC81 - 109
d_24ens_1THRPROC111 - 122
d_25ens_1ALATHRC124 - 142
d_26ens_1GLUMETC144 - 168
d_27ens_1ALAGLUC171 - 203
d_28ens_1THRLEUC205 - 226
d_29ens_1GLYASPC228 - 229
d_210ens_1PHEALAC231 - 245
d_211ens_1GLUALAC247 - 284
d_212ens_1GLUASPC286 - 388
d_213ens_1VALASPC390 - 404
d_214ens_1THRTHRC406 - 455
d_215ens_1ASNALAC458 - 461
d_216ens_1PHEARGC463 - 464
d_217ens_1PHEGLYC466 - 530
d_218ens_1GOLGOLD

NCS oper: (Code: givenMatrix: (0.854018242015, -0.132474395402, -0.503093805238), (-0.135546392492, -0.990296186796, 0.0306698206712), (-0.502274842879, 0.0419999640526, -0.863687434915)Vector: -14. ...NCS oper: (Code: given
Matrix: (0.854018242015, -0.132474395402, -0.503093805238), (-0.135546392492, -0.990296186796, 0.0306698206712), (-0.502274842879, 0.0419999640526, -0.863687434915)
Vector: -14.9476046513, 17.839098275, -59.3393265211)

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Components

#1: Protein Tryptophan 6-halogenase


Mass: 62362.312 Da / Num. of mol.: 2 / Mutation: V52I, V82I, S360T, G469S, S470N
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag from pET-28a not cleaved / Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal, thdH / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 800 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42.04 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: reservoir solution: 0.1 M Bicine pH 9.0, 10 % (w/v) PEG 4000, 5 mM tryptophan; protein buffer solution: 10 mM TRIS, 50 mM NaCl, 1 mM TCEP; protein concentration: ~15 mg/mL; drop ratio: 100 ...Details: reservoir solution: 0.1 M Bicine pH 9.0, 10 % (w/v) PEG 4000, 5 mM tryptophan; protein buffer solution: 10 mM TRIS, 50 mM NaCl, 1 mM TCEP; protein concentration: ~15 mg/mL; drop ratio: 100 nL+100 nL (protein + reservoir)

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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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2018
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 95688 / % possible obs: 99.9 % / Redundancy: 6.87 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.077 / Net I/σ(I): 14.44
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 6.97 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 7071 / CC1/2: 0.801 / Rrim(I) all: 1.182 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H43

6h43


Resolution: 1.84→49.28 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 4732 4.95 %
Rwork0.1664 90885 -
obs0.168 95617 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.05 Å2
Refinement stepCycle: LAST / Resolution: 1.84→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 12 800 9208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00428750
X-RAY DIFFRACTIONf_angle_d0.655211893
X-RAY DIFFRACTIONf_chiral_restr0.04691268
X-RAY DIFFRACTIONf_plane_restr0.00631554
X-RAY DIFFRACTIONf_dihedral_angle_d10.84673210
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.920837314008 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.31121440.29223059X-RAY DIFFRACTION99.78
1.86-1.880.35121560.28052969X-RAY DIFFRACTION99.84
1.88-1.910.29331510.26423058X-RAY DIFFRACTION99.81
1.91-1.930.28991640.25533028X-RAY DIFFRACTION99.91
1.93-1.960.31131710.24752964X-RAY DIFFRACTION99.78
1.96-1.980.26721590.24153043X-RAY DIFFRACTION99.78
1.98-2.010.27071500.23453001X-RAY DIFFRACTION99.81
2.01-2.040.28651440.21043034X-RAY DIFFRACTION99.84
2.04-2.070.2311380.20073071X-RAY DIFFRACTION99.91
2.07-2.110.24421510.18842980X-RAY DIFFRACTION99.81
2.11-2.140.24151340.18173063X-RAY DIFFRACTION99.81
2.14-2.180.23281450.17343034X-RAY DIFFRACTION99.75
2.18-2.220.23411790.17793001X-RAY DIFFRACTION99.84
2.22-2.270.19951680.17043015X-RAY DIFFRACTION99.75
2.27-2.320.22651480.16583021X-RAY DIFFRACTION99.91
2.32-2.370.24631600.17043032X-RAY DIFFRACTION99.91
2.37-2.430.1941540.16713038X-RAY DIFFRACTION99.81
2.43-2.50.22111660.16562989X-RAY DIFFRACTION99.91
2.5-2.570.22661370.16853055X-RAY DIFFRACTION99.87
2.57-2.650.22191540.16413039X-RAY DIFFRACTION99.91
2.65-2.750.20621660.15863009X-RAY DIFFRACTION99.91
2.75-2.860.19251820.15393035X-RAY DIFFRACTION99.97
2.86-2.990.21011770.16843004X-RAY DIFFRACTION99.94
2.99-3.150.21311800.18293019X-RAY DIFFRACTION99.88
3.15-3.340.21721600.16643034X-RAY DIFFRACTION99.91
3.34-3.60.14991430.15333052X-RAY DIFFRACTION99.94
3.6-3.960.18611580.15053060X-RAY DIFFRACTION99.94
3.96-4.540.13891530.12353043X-RAY DIFFRACTION99.97
4.54-5.710.15941800.12913044X-RAY DIFFRACTION99.97
5.71-49.280.18621600.1823091X-RAY DIFFRACTION99.6
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.399336968902-0.3270041950640.03773048481011.20794335713-0.03302718286420.813982966492-0.06796054364180.02550901083930.05226337433650.273583302165-0.0495987804625-0.00882599965136-0.1051975661070.01897338814130.1182565799010.375563689228-0.02916384181630.01318370316710.306459224199-0.008527852583690.296360078026-20.735590658712.9599465591-4.80158785527
20.318900115244-0.1265007973850.09865541950611.39530562748-0.2867058521720.9936170469270.02399706267420.192168731593-0.00367824633521-0.131709755751-0.009491293398880.122166745128-0.0279343067203-0.109377478322-0.008949059255130.213019682405-0.016411928090.04078924675430.4222330970790.01111383520750.299949983375-31.84410476048.0403655566-44.2173862901
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain 'A'AA - B0 - 601
22chain 'B'BC - D-5 - 601

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