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- PDB-3wku: Crystal structure of the anaerobic DesB-gallate complex -

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Basic information

Entry
Database: PDB / ID: 3wku
TitleCrystal structure of the anaerobic DesB-gallate complex
ComponentsGallate dioxygenase
KeywordsOXIDOREDUCTASE / type II extradiol dioxygenase / domain-swap dimer / extradiol dioxygenase / Fe2+ binding
Function / homology
Function and homology information


oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / 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 / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase ...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 / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / Dioxygenase LigAB, LigA subunit superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 3,4,5-trihydroxybenzoic acid / Gallate dioxygenase
Similarity search - Component
Biological speciesSphingobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionOct 31, 2013Deposition 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 1.2Mar 20, 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_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_alt_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.pdbx_ptnr2_label_alt_id / _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_label_asym_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)94,1885
Polymers93,9062
Non-polymers2823
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-80 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.435, 60.765, 117.986
Angle α, β, γ (deg.)90.00, 98.58, 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.) Sphingobium (bacteria) / Strain: SYK-6 / Gene: desB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G2IKE5, linoleate 9S-lipoxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GDE / 3,4,5-trihydroxybenzoic acid / Gallate


Mass: 170.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→56.8 Å / Num. all: 43335 / Num. obs: 42572 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.0309 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.859 / SU B: 18.891 / SU ML: 0.397 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31436 1098 5 %RANDOM
Rwork0.23287 ---
all0.23694 20862 --
obs0.23694 20862 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: 61.634 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20.22 Å2
2--2.36 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 14 2 6465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226650
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9459020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85923.394327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.771151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1781546
X-RAY DIFFRACTIONr_chiral_restr0.090.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215220
X-RAY DIFFRACTIONr_mcbond_it0.5331.54037
X-RAY DIFFRACTIONr_mcangle_it0.99126470
X-RAY DIFFRACTIONr_scbond_it1.2232613
X-RAY DIFFRACTIONr_scangle_it2.0354.52550
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 80 -
Rwork0.264 1520 -
obs--100 %

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