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- PDB-3das: Structure of the PQQ-bound form of Aldose Sugar Dehydrogenase (Ad... -

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Basic information

Entry
Database: PDB / ID: 3das
TitleStructure of the PQQ-bound form of Aldose Sugar Dehydrogenase (Adh) from Streptomyces coelicolor
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / aldose sugar dehydrogenase / beta propellor / PQQ / sGDH
Function / homology
Function and homology information


Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Soluble quinoprotein glucose/sorbosone dehydrogenase / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
alpha-L-arabinopyranose / PYRROLOQUINOLINE QUINONE / Putative oxidoreductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSouthall, S.M. / Doel, J.J. / Oubrie, A. / Richardson, D.J.
CitationJournal: To be Published
Title: Structural and Enzymatic Characterization of a Thermostable PQQ-dependent Soluble Aldose Sugar Dehydrogenase
Authors: Southall, S.M. / Doel, J.J. / Oubrie, A. / Richardson, D.J.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,99814
Polymers36,7911
Non-polymers1,20713
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.033, 41.260, 85.931
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Putative oxidoreductase


Mass: 36790.770 Da / Num. of mol.: 1 / Fragment: sequence database residues 104-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z571
#2: Sugar ChemComp-ARA / alpha-L-arabinopyranose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinopyranoseCOMMON NAMEGMML 1.0
a-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 492 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 20% PEG 6000, 0.1M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9184 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 43328 / Num. obs: 43328 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→48.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.515 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.121 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The authors state that in remark 500, the waters are indeed alternative conformations of the ligands and their occupancies are correctly set at 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.15939 2249 5.2 %RANDOM
Rwork0.13238 ---
obs0.13378 41068 94.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.05 Å2
2--0.31 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 78 490 3339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.282.0014058
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2824.044136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63415496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7941525
X-RAY DIFFRACTIONr_chiral_restr0.0830.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022357
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21356
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21952
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2437
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6461.51850
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95622915
X-RAY DIFFRACTIONr_scbond_it1.43431321
X-RAY DIFFRACTIONr_scangle_it2.0864.51097
X-RAY DIFFRACTIONr_rigid_bond_restr0.81633171
X-RAY DIFFRACTIONr_sphericity_free2.4553492
X-RAY DIFFRACTIONr_sphericity_bonded1.44232847
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 129 -
Rwork0.138 2229 -
obs--69.76 %

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