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- PDB-3wr8: Crystal structure of DesB from Sphingobium sp. strain SYK-6 -

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Basic information

Entry
Database: PDB / ID: 3wr8
TitleCrystal structure of DesB from Sphingobium sp. strain SYK-6
ComponentsGallate dioxygenase
KeywordsOXIDOREDUCTASE / EXTRADIOL DIOXYGENASE / FE2+ BINDING / DOMAIN-SWAP DIMER
Function / homology
Function and homology information


dioxygenase activity / ferrous iron binding
Similarity search - Function
Gallate dioxygenase, N-terminal / Gallate dioxygenase, C-terminal / Protocatechuate 4,5-dioxygenase; Chain A / Dioxygenase LigAB, LigA subunit / Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Dioxygenase LigAB, LigA subunit superfamily / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B ...Gallate dioxygenase, N-terminal / Gallate dioxygenase, C-terminal / Protocatechuate 4,5-dioxygenase; Chain A / Dioxygenase LigAB, LigA subunit / Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / Dioxygenase LigAB, LigA subunit superfamily / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Gallate dioxygenase / Gallate dioxygenase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSugimoto, K. / Senda, M. / Kasai, D. / Fukuda, M. / Masai, E. / Senda, T.
CitationJournal: Plos One / Year: 2014
Title: Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Authors: Sugimoto, K. / Senda, M. / Kasai, D. / Fukuda, M. / Masai, E. / Senda, T.
History
DepositionFeb 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.2Nov 8, 2023Group: 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: Gallate dioxygenase
B: Gallate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0184
Polymers93,9062
Non-polymers1122
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-68 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.420, 64.916, 116.247
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gallate dioxygenase / DESB / TYPE II EXTRADIOL DIOXYGENASE


Mass: 46953.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK-6 / Gene: desB / Plasmid: PEVK3G / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q5NTE5, UniProt: G2IKE5*PLUS, linoleate 9S-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 25% PEG8000, 0.1M SODIUM ACETATE, 0.1M HEPES-NAOH, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→56.63 Å / Num. all: 40016 / Num. obs: 39856 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.64 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.22
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.69 % / Mean I/σ(I) obs: 4.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BOU

1bou


Resolution: 2.25→56.63 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.373 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1994 5 %RANDOM
Rwork0.191 ---
all0.193 37880 --
obs0.193 37880 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.25 Å2
2--0.67 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→56.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6458 0 2 282 6742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9439017
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97823.435329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.096151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3461546
X-RAY DIFFRACTIONr_chiral_restr0.0840.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215222
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5271.54043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0426478
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.72632605
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8874.52539
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 145 -
Rwork0.228 2749 -
obs--100 %

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