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- PDB-3auu: Crystal structure of Bacillus megaterium glucose dehydrogenase 4 ... -

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Basic information

Entry
Database: PDB / ID: 3auu
TitleCrystal structure of Bacillus megaterium glucose dehydrogenase 4 in complex with D-glucose
ComponentsGlucose 1-dehydrogenase 4
KeywordsOXIDOREDUCTASE / Rossmann Fold / NAD / Oxidation-reduction process / cytosol
Function / homology
Function and homology information


glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)] activity / identical protein binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Glucose 1-dehydrogenase 4
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNishioka, T. / Yasutake, Y. / Nishiya, Y. / Tamura, T.
CitationJournal: Febs J. / Year: 2012
Title: Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV
Authors: Nishioka, T. / Yasutake, Y. / Nishiya, Y. / Tamura, T.
History
DepositionFeb 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
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 / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose 1-dehydrogenase 4
B: Glucose 1-dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7584
Polymers58,3982
Non-polymers3602
Water2,792155
1
A: Glucose 1-dehydrogenase 4
B: Glucose 1-dehydrogenase 4
hetero molecules

A: Glucose 1-dehydrogenase 4
B: Glucose 1-dehydrogenase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5178
Polymers116,7964
Non-polymers7214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area16870 Å2
ΔGint-130 kcal/mol
Surface area32610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.032, 127.525, 64.519
Angle α, β, γ (deg.)90.00, 109.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glucose 1-dehydrogenase 4 / / GLCDH-IV


Mass: 29199.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: IAM 1030 / Gene: gdhIV / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: P39485, glucose 1-dehydrogenase [NAD(P)+]
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 0.2M magnesium chloride, 51% PEG 200, 400mM D-glucose, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 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→50 Å / Num. obs: 33134 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 3318 / Rsym value: 0.398 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.989 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25719 1667 5 %RANDOM
Rwork0.20505 ---
obs0.20761 31376 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.163 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å2-0.24 Å2
2--1.33 Å20 Å2
3----3.03 Å2
Refinement stepCycle: LAST / Resolution: 2→28.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 24 155 4153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9655551
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.84125.932177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06215692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3141512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213086
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_it0.6261.52604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11224189
X-RAY DIFFRACTIONr_scbond_it1.65731488
X-RAY DIFFRACTIONr_scangle_it2.6854.51360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 113 -
Rwork0.27 2321 -
obs--99.47 %

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