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- PDB-3wr4: Crystal structure of the anaerobic DesB-gallate complex -

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Basic information

Entry
Database: PDB / ID: 3wr4
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: 2.4 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 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-81 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.303, 63.905, 118.295
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gallate 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, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#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

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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: 47.2 %
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: 1.73912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73912 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 66303 / Num. obs: 56954 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 40.14 Å2
Reflection shellResolution: 2.4→2.52 Å / % possible all: 66.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: dev_1539)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WKU

3wku


Resolution: 2.4→19.99 Å / FOM work R set: 0.6929 / SU ML: 0.46 / σ(F): 1.35 / Phase error: 36.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2946 1583 5.03 %Random
Rwork0.2214 ---
all0.2252 ---
obs0.2252 31674 86.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.66 Å2 / Biso mean: 51.9 Å2 / Biso min: 21.39 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 14 0 6463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096650
X-RAY DIFFRACTIONf_angle_d1.3149020
X-RAY DIFFRACTIONf_chiral_restr0.051932
X-RAY DIFFRACTIONf_plane_restr0.0061188
X-RAY DIFFRACTIONf_dihedral_angle_d15.5812408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.44130.42891140.35911984209864
2.4413-2.48560.44741090.33572114222367
2.4856-2.53340.39391090.30682195230470
2.5334-2.5850.37611250.31372341246675
2.585-2.6410.41821290.31912336246574
2.641-2.70230.39081290.31092468259779
2.7023-2.76980.39971310.29332557268881
2.7698-2.84440.39251340.27752651278585
2.8444-2.92790.40951490.27222731288086
2.9279-3.02210.30651500.28242772292289
3.0221-3.12970.39921460.2772873301991
3.1297-3.25450.37831490.25372895304492
3.2545-3.40190.30331550.24092944309994
3.4019-3.58030.29681590.22392989314894
3.5803-3.80320.29681580.21363008316695
3.8032-4.09450.23071560.20752996315296
4.0945-4.50230.24381640.17432986315096
4.5023-5.14410.25561640.17793050321497
5.1441-6.44480.24751650.18613111327699
6.4448-19.99110.22751690.15593077324698

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