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- PDB-1gco: CRYSTAL STRUCTURE OF GLUCOSE DEHYDROGENASE COMPLEXED WITH NAD+ -

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Basic information

Entry
Database: PDB / ID: 1gco
TitleCRYSTAL STRUCTURE OF GLUCOSE DEHYDROGENASE COMPLEXED WITH NAD+
ComponentsGLUCOSE 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 / Resolution: 1.7 Å
AuthorsYamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S.
Citation
Journal: J.Biochem. / 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Bacillus megaterium IWG3
Authors: Yamamoto, K. / Kusunoki, M. / Urabe, I. / Tabata, S. / Osaki, S.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation ..._pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3]
Revision 1.4Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: GLUCOSE DEHYDROGENASE
B: GLUCOSE DEHYDROGENASE
E: GLUCOSE DEHYDROGENASE
F: GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1068
Polymers112,4524
Non-polymers2,6544
Water10,124562
1
A: GLUCOSE DEHYDROGENASE
B: GLUCOSE DEHYDROGENASE
hetero molecules

A: GLUCOSE DEHYDROGENASE
B: GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1068
Polymers112,4524
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area21510 Å2
ΔGint-149 kcal/mol
Surface area32370 Å2
MethodPISA
2
E: GLUCOSE DEHYDROGENASE
F: GLUCOSE DEHYDROGENASE
hetero molecules

E: GLUCOSE DEHYDROGENASE
F: GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1068
Polymers112,4524
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area21530 Å2
ΔGint-146 kcal/mol
Surface area32340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.675, 66.557, 119.528
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GLUCOSE DEHYDROGENASE


Mass: 28112.963 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: IWG3 / Plasmid: PKP1500 / 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.: 562 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG2000, sodium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 294 K
Details: used microseeding, Yamamoto, K., (2000) Acta Crystallogr., Sect.D, 56, 1443.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
240 mMsodium phosphate1drop
328 %(w/v)PEG20001reservoir
44 mMNAD+1reservoir
540 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 357354 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 3.77 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.166 / Num. unique all: 8013 / % possible all: 77.3
Reflection
*PLUS
Num. obs: 94821 / Num. measured all: 357354
Reflection shell
*PLUS
% possible obs: 77.3 % / Mean I/σ(I) obs: 11.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→34.39 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2894287.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.192 4979 5 %RANDOM
Rwork0.178 ---
obs0.178 94583 90.7 %-
all-94821 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5391 Å2 / ksol: 0.314666 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7888 0 176 562 8626
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it0.791.5
X-RAY DIFFRACTIONc_mcangle_it1.232
X-RAY DIFFRACTIONc_scbond_it1.522
X-RAY DIFFRACTIONc_scangle_it2.232.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 668 5 %
Rwork0.216 12803 -
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it0.791.5
X-RAY DIFFRACTIONc_scbond_it1.522
X-RAY DIFFRACTIONc_mcangle_it1.232
X-RAY DIFFRACTIONc_scangle_it2.232.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.241 / % reflection Rfree: 5 % / Rfactor Rwork: 0.216

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