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- PDB-6frl: BrvH, a flavin-dependent halogenase from Brevundimonas sp. BAL3 -

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Basic information

Entry
Database: PDB / ID: 6frl
TitleBrvH, a flavin-dependent halogenase from Brevundimonas sp. BAL3
ComponentsTryptophan halogenase superfamily
KeywordsFLAVOPROTEIN / flavin-dependent halogenase
Function / homology
Function and homology information


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
L(+)-TARTARIC ACID / Tryptophan halogenase superfamily
Similarity search - Component
Biological speciesBrevundimonas sp. BAL3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWidmann, C. / Neubauer, P.R. / Sewald, N. / Niemann, H.H.
CitationJournal: PLoS ONE / Year: 2018
Title: A flavin-dependent halogenase from metagenomic analysis prefers bromination over chlorination.
Authors: Neubauer, P.R. / Widmann, C. / Wibberg, D. / Schroder, L. / Frese, M. / Kottke, T. / Kalinowski, J. / Niemann, H.H. / Sewald, N.
History
DepositionFeb 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 halogenase superfamily
B: Tryptophan halogenase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8358
Polymers112,9602
Non-polymers8756
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-3 kcal/mol
Surface area38500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.620, 88.350, 70.110
Angle α, β, γ (deg.)90.00, 99.07, 90.00
Int Tables number5
Space group name H-MC121
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: 6 - 501 / Label seq-ID: 8 - 503

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Tryptophan halogenase superfamily


Mass: 56479.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas sp. BAL3 (bacteria) / Gene: BBAL3_2452 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4WBL8
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.45 Å3/Da / Density % sol: 49.75 % / Description: Small plates
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.95 M Na/K tartrate, 0.1 M MES pH 6 streak seeding protein concentration 10 mg/ml drop size 2 uL drop ratio (protein:reservoir) 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→89.18 Å / Num. obs: 36507 / % possible obs: 96.5 % / Redundancy: 11.4 % / CC1/2: 0.996 / Rrim(I) all: 0.202 / Net I/σ(I): 11.89
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.84 / Num. unique obs: 2688 / CC1/2: 0.661 / Rrim(I) all: 1.422 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2aqj, 2wet, 2oal, 5hy5

2aqj

2wet

2oal

5hy5


Resolution: 2.5→89.18 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.656 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.941 / ESU R Free: 0.299 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24072 1809 5 %RANDOM
Rwork0.19456 ---
obs0.19687 34697 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.358 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20.16 Å2
2--1.36 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.5→89.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7719 0 56 315 8090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197998
X-RAY DIFFRACTIONr_bond_other_d0.0010.027360
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.95310864
X-RAY DIFFRACTIONr_angle_other_deg0.998316931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54921.875384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.352151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5261591
X-RAY DIFFRACTIONr_chiral_restr0.0860.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021846
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_it2.9693.8283933
X-RAY DIFFRACTIONr_mcbond_other2.9693.8263932
X-RAY DIFFRACTIONr_mcangle_it4.6895.7324911
X-RAY DIFFRACTIONr_mcangle_other4.6895.7344912
X-RAY DIFFRACTIONr_scbond_it3.1594.1624065
X-RAY DIFFRACTIONr_scbond_other3.1574.1634065
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0926.1235954
X-RAY DIFFRACTIONr_long_range_B_refined7.23343.38642
X-RAY DIFFRACTIONr_long_range_B_other7.23443.3048643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 31262 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 133 -
Rwork0.323 2548 -
obs--97.74 %

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