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- PDB-3oul: Crystal Structure of toxoflavin-degrading enzyme in a substrate-f... -

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Basic information

Entry
Database: PDB / ID: 3oul
TitleCrystal Structure of toxoflavin-degrading enzyme in a substrate-free form
ComponentsToxoflavin-degrading enzyme
KeywordsTOXOFLAVIN BINDING PROTEIN / Toxoflavin / phytotoxin-degrading enzyme / Paenibacillus polymyxa JH2 / toxoflavin-degrading enzyme
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKim, M.I. / Rhee, S.
CitationJournal: Plos One / Year: 2011
Title: Structural and functional analysis of phytotoxin toxoflavin-degrading enzyme
Authors: Jung, W.S. / Lee, J. / Kim, M.I. / Ma, J. / Nagamatsu, T. / Goo, E. / Kim, H. / Hwang, I. / Han, J. / Rhee, S.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.pdbx_leaving_atom_flag / _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-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2192
Polymers26,1641
Non-polymers551
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.377, 110.377, 56.787
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Toxoflavin-degrading enzyme


Mass: 26163.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus polymyxa (bacteria) / Strain: JH2 / Plasmid: pET41b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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.: 134 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS PROTEIN IS D175A MUTANT.

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M CAPS, pH 10.5, 0.2M LiSO4, 1.2M NaH2PO4/0.8M K2HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2007
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 34046 / Num. obs: 32823 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.275 / Num. unique all: 3014 / % possible all: 88.5

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure from MAD data using a different mutant

Resolution: 1.6→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.2197 3030 8.9 %
Rwork0.195 --
all-34046 -
obs-30441 89.4 %
Solvent computationBsol: 42.6794 Å2
Displacement parametersBiso max: 52.84 Å2 / Biso mean: 23.1325 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1-5.087 Å21.936 Å20 Å2
2--5.087 Å20 Å2
3----10.174 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 1 134 1872
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2151.5
X-RAY DIFFRACTIONc_scbond_it2.2132
X-RAY DIFFRACTIONc_mcangle_it1.8052
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 1.6→1.66 Å /
Num. reflection% reflection
obs3014 88.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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