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- PDB-1rwb: Cooperative Effect of Two Surface Amino Acid Mutations (Q252L and... -

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Basic information

Entry
Database: PDB / ID: 1rwb
TitleCooperative Effect of Two Surface Amino Acid Mutations (Q252L and E170K) of Glucose Dehydrogenase from Bacillus megaterium IWG3 for the stabilization of Oligomeric State
ComponentsGlucose 1-dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / sporulation resulting in formation of a cellular spore
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body / Resolution: 2 Å
AuthorsBaik, S.-H. / Michel, F. / Haser, R. / Harayama, S.
CitationJournal: Appl.Environ.Microbiol. / Year: 2005
Title: Cooperative effect of two surface amino acid mutations (Q252L and E170K) in glucose dehydrogenase from Bacillus megaterium IWG3 on stabilization of its oligomeric state.
Authors: Baik, S.H. / Michel, F. / Aghajari, N. / Haser, R. / Harayama, S.
History
DepositionDec 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose 1-dehydrogenase
B: Glucose 1-dehydrogenase
E: Glucose 1-dehydrogenase
F: Glucose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0468
Polymers112,3924
Non-polymers2,6544
Water9,782543
1
A: Glucose 1-dehydrogenase
B: Glucose 1-dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)115,0468
Polymers112,3924
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area21420 Å2
ΔGint-150 kcal/mol
Surface area31720 Å2
MethodPQS
2
E: Glucose 1-dehydrogenase
F: Glucose 1-dehydrogenase
hetero molecules

E: Glucose 1-dehydrogenase
F: Glucose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0468
Polymers112,3924
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area21280 Å2
ΔGint-153 kcal/mol
Surface area31450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)118.500, 65.400, 118.000
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glucose 1-dehydrogenase


Mass: 28098.057 Da / Num. of mol.: 4 / Mutation: Q252L, E170K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: IWG3 / Production host: Escherichia coli (E. coli)
References: UniProt: P40288, glucose 1-dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme1drop
24 mMNAD+1reservoir
350 mMsodium phosphate1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2002
RadiationMonochromator: two crystal monochromator between two cylindrical parabolic mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.83→40 Å / Num. obs: 78937 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.06 / Net I/σ(I): 7
Reflection shellResolution: 1.83→1.92 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2274 / Rsym value: 0.19 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. obs: 61998 / Redundancy: 3.1 % / Num. measured all: 193166 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 5.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: Rigid Body
Starting model: PDB Entry 1GCO

1gco


Resolution: 2→14.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2792389.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 6090 10 %RANDOM
Rwork0.224 ---
obs0.224 60614 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.2644 Å2 / ksol: 0.356288 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å2-6.33 Å2
2--2.91 Å20 Å2
3----4.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7884 0 176 543 8603
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 948 9.4 %
Rwork0.285 9146 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2WATER.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3NAD.PARAM&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4DNA-RNA.PARAM&_1_TOPOLOGY_INFILE_4
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14

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