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- PDB-3pkw: Crystal Structure of Toxoflavin Lyase (TflA) bound to Mn(II) -

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Basic information

Entry
Database: PDB / ID: 3pkw
TitleCrystal Structure of Toxoflavin Lyase (TflA) bound to Mn(II)
ComponentsToxoflavin lyase (TflA)
KeywordsLYASE / Metalloenzyme / Vicinal oxygen chelate superfamily
Function / homology
Function and homology information


Toxoflavin-degrading enzyme / Toxoflavin-degrading enzyme / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / Toxoflavin degrading enzyme
Similarity search - Component
Biological speciesPaenibacillus Polymyxa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsFenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2011
Title: Toxoflavin lyase requires a novel 1-his-2-carboxylate facial triad .
Authors: Fenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E.
History
DepositionNov 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxoflavin lyase (TflA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3832
Polymers28,3281
Non-polymers551
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.856, 110.856, 55.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

21A-365-

HOH

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Components

#1: Protein Toxoflavin lyase (TflA)


Mass: 28327.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus Polymyxa (bacteria) / Strain: JH2 / Gene: tflA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3SET7*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS (pH 10.5), 0.2M Li2SO4, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9177 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 13, 2010
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 17.31 / Number: 136728 / Rmerge(I) obs: 0.07 / Χ2: 1.47 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 29332 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665099.310.0483.6134.7
2.913.6699.910.0581.7194.6
2.542.9110010.0841.4474.7
2.312.5410010.0851.294.7
2.142.3110010.0911.2614.7
2.022.1410010.1091.1934.7
1.912.0210010.1511.1434.7
1.831.9110010.1991.0074.7
1.761.8310010.2941.0324.6
1.71.7610010.4171.0554.6
ReflectionResolution: 1.8→50 Å / Num. obs: 23624 / % possible obs: 99.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.054 / Χ2: 1.057 / Net I/σ(I): 23.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.863.70.37123601.08100
1.86-1.943.80.26323771.063100
1.94-2.033.90.1923661.063100
2.03-2.133.90.13823881.086100
2.13-2.273.90.10323521.044100
2.27-2.4440.08123771.005100
2.44-2.6940.06523701.076100
2.69-3.0840.04823811.046100
3.08-3.884.10.03623621.05499.6
3.88-5040.03422911.05696.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→24.1 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.22 / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 1120 4.98 %
Rwork0.1892 --
obs0.1909 22470 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.809 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 78.28 Å2 / Biso mean: 29.6777 Å2 / Biso min: 13.76 Å2
Baniso -1Baniso -2Baniso -3
1--7.885 Å20 Å20 Å2
2---7.885 Å2-0 Å2
3---15.7701 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 1 147 1858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071764
X-RAY DIFFRACTIONf_angle_d1.0792405
X-RAY DIFFRACTIONf_chiral_restr0.07273
X-RAY DIFFRACTIONf_plane_restr0.004318
X-RAY DIFFRACTIONf_dihedral_angle_d14.737634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.88010.34171010.25912430253186
1.8801-1.97920.25771500.22682511266190
1.9792-2.10310.22411340.21352658279294
2.1031-2.26540.22721400.19732708284896
2.2654-2.49320.26171560.20052718287497
2.4932-2.85340.25641420.20072785292798
2.8534-3.59310.21951450.18362781292699
3.5931-24.10240.16921520.15612759291198

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