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- PDB-1g6k: Crystal structure of glucose dehydrogenase mutant E96A complexed ... -

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Basic information

Entry
Database: PDB / ID: 1g6k
TitleCrystal structure of glucose dehydrogenase mutant E96A complexed with NAD+
ComponentsGLUCOSE 1-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductase
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S.
Citation
Journal: To be Published
Title: Structural analysis of stability-increasing mutants of glucose dehydrogenase
Authors: Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S.
#1: Journal: J.BIOCHEM.(TOKYO) / Year: 2001
Title: Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution
Authors: Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Bacillus megaterium IWG3
Authors: Yamaoto, K. / Kusunoki, M. / Urabe, I. / Tabata, S. / Osaki, S.
History
DepositionNov 6, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 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

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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)114,8738
Polymers112,2204
Non-polymers2,6544
Water5,603311
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)114,8738
Polymers112,2204
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area21380 Å2
ΔGint-158 kcal/mol
Surface area33630 Å2
MethodPISA, PQS
2
E: GLUCOSE 1-DEHYDROGENASE
F: GLUCOSE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4374
Polymers56,1102
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21450 Å2
ΔGint-155 kcal/mol
Surface area33560 Å2
MethodPISA
3
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)114,8738
Polymers112,2204
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)121.955, 66.640, 120.065
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological active form is tetramer. For tetramer1, apply (-x, y, -z)+a to chains A and B. For tetramer2, apply (-x, y, -z)+c to chains E and F.

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Components

#1: Protein
GLUCOSE 1-DEHYDROGENASE


Mass: 28054.924 Da / Num. of mol.: 4 / Mutation: E96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: IWG3 / Plasmid: PKP1500 / Production host: Escherichia coli (E. coli) / Strain (production host): KP3998
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.: 311 / 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: 2.08 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG2000, sodium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 294512 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 4.78 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.208 / Num. unique all: 5172 / % possible all: 80.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCO

1gco


Resolution: 2→39.95 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3059 -RANDOM
Rwork0.219 ---
all-65194 --
obs-61350 94 %-
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å2-0.82 Å2
2--5.62 Å20 Å2
3----7.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 176 311 8359
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.77

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