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- PDB-3ay7: Crystal structure of Bacillus megaterium glucose dehydrogenase 4 ... -

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Basic information

Entry
Database: PDB / ID: 3ay7
TitleCrystal structure of Bacillus megaterium glucose dehydrogenase 4 G259A mutant
ComponentsGlucose 1-dehydrogenase 4
KeywordsOXIDOREDUCTASE / Rossmann Fold / Oxidation-reduction process / Nucleotide binding / Cytosol
Function / homology
Function and homology information


glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / 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
Glucose 1-dehydrogenase 4
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionApr 29, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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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)58,4623
Polymers58,4262
Non-polymers351
Water4,035224
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)116,9236
Polymers116,8524
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area15590 Å2
ΔGint-138 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.116, 128.260, 64.641
Angle α, β, γ (deg.)90.00, 110.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 29213.094 Da / Num. of mol.: 2 / Mutation: G259A
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 0.2M magnesium chloride, 50.5% PEG 200, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 38880 / Num. obs: 38880 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 3.67
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.67 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.971 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24583 1949 5 %RANDOM
Rwork0.19976 ---
obs0.20201 36898 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.517 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 1 224 4164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224027
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9575463
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5655521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.8926.114175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70715683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9131510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213044
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_it0.6011.52578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07424150
X-RAY DIFFRACTIONr_scbond_it1.57231449
X-RAY DIFFRACTIONr_scangle_it2.5744.51312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 141 -
Rwork0.277 2648 -
obs--97.45 %

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