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- PDB-7cu1: CRYSTAL STRUCTURE OF STREPTOMYCES ALBOGRISEOLUS FLAVIN-DEPENDENT ... -

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Basic information

Entry
Database: PDB / ID: 7cu1
TitleCRYSTAL STRUCTURE OF STREPTOMYCES ALBOGRISEOLUS FLAVIN-DEPENDENT TRYPTOPHAN 6-HALOGENASE (THAL) IN COMPLEX WITH FAD and AMP
ComponentsTryptophan 6-halogenase
KeywordsOXIDOREDUCTASE / FLAVIN MONOOXYGENASE / FLAVIN-DEPENDENT TRYPTOPHAN 6-HALOGENASE
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
ADENOSINE MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 6-halogenase ThaL
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
Model detailsCrystal structure of flavin-dependent tryptophan 6-halogenase (Thal) in complex with FAD from ...Crystal structure of flavin-dependent tryptophan 6-halogenase (Thal) in complex with FAD from Streptomyces albogriseolus
AuthorsChitnumsub, P. / Jaruwat, A. / Phintha, A. / Chaiyen, P.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Dissecting the low catalytic capability of flavin-dependent halogenases.
Authors: Phintha, A. / Prakinee, K. / Jaruwat, A. / Lawan, N. / Visitsatthawong, S. / Kantiwiriyawanitch, C. / Songsungthong, W. / Trisrivirat, D. / Chenprakhon, P. / Mulholland, A. / van Pee, K.H. / ...Authors: Phintha, A. / Prakinee, K. / Jaruwat, A. / Lawan, N. / Visitsatthawong, S. / Kantiwiriyawanitch, C. / Songsungthong, W. / Trisrivirat, D. / Chenprakhon, P. / Mulholland, A. / van Pee, K.H. / Chitnumsub, P. / Chaiyen, P.
History
DepositionAug 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: 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)125,6594
Polymers124,5262
Non-polymers1,1332
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-21 kcal/mol
Surface area38990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.553, 118.151, 82.863
Angle α, β, γ (deg.)90.000, 100.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tryptophan 6-halogenase


Mass: 62263.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal, thdH / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.66 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: microbatch / pH: 7 / Details: 0.28-0.38M NaF, 23-31% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.91→20.64 Å / Num. obs: 77292 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.081 / Net I/σ(I): 16.9 / Num. measured all: 547491
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.465 / Num. measured all: 15402 / Num. unique obs: 3948 / CC1/2: 0.834 / Rpim(I) all: 0.253 / Rrim(I) all: 0.533 / Net I/σ(I) obs: 3.3 / % possible all: 86.2

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HY5

5hy5


Resolution: 1.91→20.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.005 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3807 4.9 %RANDOM
Rwork0.174 ---
obs0.177 73446 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 99.24 Å2 / Biso mean: 17.63 Å2 / Biso min: 5.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0.84 Å2
2---0.35 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.91→20.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8438 0 76 731 9245
Biso mean--23.87 24.27 -
Num. residues----1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0148749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177625
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.66711887
X-RAY DIFFRACTIONr_angle_other_deg0.9411.6417847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96251055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08221.548491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.112151389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5091565
X-RAY DIFFRACTIONr_chiral_restr0.0710.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021750
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 222 -
Rwork0.278 4803 -
all-5025 -
obs--88.75 %

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