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

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Basic information

Entry
Database: PDB / ID: 7aqu
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 / 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
ALANINE / GLYCINE / SERINE / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 / 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)126,06817
Polymers124,7252
Non-polymers1,34315
Water17,565975
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-4 kcal/mol
Surface area38510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.580, 118.570, 87.100
Angle α, β, γ (deg.)90.000, 104.038, 90.000
Int Tables number4
Space group name H-MP1211
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: 22 - 549

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: 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

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Non-polymers , 6 types, 990 molecules

#2: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.51 % / Description: Hexagonal
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 9
Details: reservoir solution: 0.1 M bicine pH 9.0, 20 % (w/v) PEG 4000, 10 % (v/v) glycerol, 0.02 M amino acid mix consisting of L-Glu, L-Ala, D-Ala, Gly, L-Lys, D-Lysis, L-Ser and D-Ser; protein ...Details: reservoir solution: 0.1 M bicine pH 9.0, 20 % (w/v) PEG 4000, 10 % (v/v) glycerol, 0.02 M amino acid mix consisting of L-Glu, L-Ala, D-Ala, Gly, L-Lys, D-Lysis, L-Ser and D-Ser; 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: 1.63→50 Å / Num. obs: 129082 / % possible obs: 96.6 % / Redundancy: 7.03 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.079 / Net I/σ(I): 15.33
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 6.73 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 8424 / CC1/2: 0.748 / Rrim(I) all: 1.146 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H43 chain A

6h43


Resolution: 1.63→48.579 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.211 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2023 6474 5.017 %
Rwork0.1667 122573 -
all0.168 --
obs-129047 96.564 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.086 Å20 Å2-0.784 Å2
2---0.923 Å20 Å2
3---0.203 Å2
Refinement stepCycle: LAST / Resolution: 1.63→48.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8383 0 88 975 9446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138917
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178068
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.64812115
X-RAY DIFFRACTIONr_angle_other_deg1.4571.5818693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76851098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20321.699512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.837151434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4051567
X-RAY DIFFRACTIONr_chiral_restr0.0840.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022049
X-RAY DIFFRACTIONr_nbd_refined0.220.21809
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.27750
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24457
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2765
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2990.216
X-RAY DIFFRACTIONr_nbd_other0.1960.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.222
X-RAY DIFFRACTIONr_mcbond_it2.3562.6634326
X-RAY DIFFRACTIONr_mcbond_other2.3432.6624325
X-RAY DIFFRACTIONr_mcangle_it3.1973.9745419
X-RAY DIFFRACTIONr_mcangle_other3.1983.9745420
X-RAY DIFFRACTIONr_scbond_it3.0562.974591
X-RAY DIFFRACTIONr_scbond_other3.0542.9694590
X-RAY DIFFRACTIONr_scangle_it4.5814.3396687
X-RAY DIFFRACTIONr_scangle_other4.5794.3396687
X-RAY DIFFRACTIONr_lrange_it6.33832.47510561
X-RAY DIFFRACTIONr_lrange_other6.33932.47810562
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.0518271
Refine LS restraints NCS

Ens-ID: 1 / Number: 18271 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.6720.3044380.2917970X-RAY DIFFRACTION85.2565
1.672-1.7180.2874910.268737X-RAY DIFFRACTION95.8554
1.718-1.7680.2854690.2438524X-RAY DIFFRACTION96.3364
1.768-1.8220.2434460.2268315X-RAY DIFFRACTION96.5293
1.822-1.8820.2554160.2078105X-RAY DIFFRACTION96.7087
1.882-1.9480.2264030.1937811X-RAY DIFFRACTION96.7377
1.948-2.0220.2183710.1787631X-RAY DIFFRACTION97.2178
2.022-2.1040.2183510.1767357X-RAY DIFFRACTION97.3724
2.104-2.1980.2243610.1756994X-RAY DIFFRACTION97.6371
2.198-2.3050.213670.1656707X-RAY DIFFRACTION97.371
2.305-2.4290.23220.1626422X-RAY DIFFRACTION98.0518
2.429-2.5770.2062960.1566161X-RAY DIFFRACTION98.2352
2.577-2.7540.2193210.1545689X-RAY DIFFRACTION98.3633
2.754-2.9750.1853180.155312X-RAY DIFFRACTION98.3578
2.975-3.2580.172730.1474947X-RAY DIFFRACTION98.7701
3.258-3.6420.1772220.1494507X-RAY DIFFRACTION98.9745
3.642-4.2040.1792110.143964X-RAY DIFFRACTION99.1686
4.204-5.1460.1691750.1373343X-RAY DIFFRACTION98.848
5.146-7.2640.2461490.1862611X-RAY DIFFRACTION99.4236
7.264-48.5790.14740.1771466X-RAY DIFFRACTION98.6547

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