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- PDB-3wic: Structure of a substrate/cofactor-unbound glucose dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3wic
TitleStructure of a substrate/cofactor-unbound glucose dehydrogenase
ComponentsGlucose 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


non-phosphorylated glucose catabolic process / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / D-glucose binding / NADP+ binding / NAD+ binding / zinc ion binding
Similarity search - Function
Glucose 1-dehydrogenase, archaea / Glucose dehydrogenase, C-terminal / Glucose dehydrogenase C-terminus / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Glucose 1-dehydrogenase, archaea / Glucose dehydrogenase, C-terminal / Glucose dehydrogenase C-terminus / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSakuraba, H. / Kanoh, Y. / Yoneda, K. / Ohshima, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium.
Authors: Kanoh, Y. / Uehara, S. / Iwata, H. / Yoneda, K. / Ohshima, T. / Sakuraba, H.
History
DepositionSep 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Glucose 1-dehydrogenase
C: Glucose 1-dehydrogenase
D: Glucose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,07426
Polymers161,1884
Non-polymers2,88622
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20220 Å2
ΔGint-213 kcal/mol
Surface area51440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.088, 122.175, 87.428
Angle α, β, γ (deg.)90.000, 109.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glucose 1-dehydrogenase / GDH / GlcDH


Mass: 40296.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea)
Strain: ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1
Gene: gdh, TV1048, TVG1073292 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q979W2, glucose 1-dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, 1,2-propanediol, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 9, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 48068 / Num. obs: 48068 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.64 Å / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DMphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cd9

2cd9


Resolution: 2.6→49.08 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.885 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 2432 5.1 %RANDOM
Rwork0.2049 ---
all0.2075 48068 --
obs0.2075 48043 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.78 Å2 / Biso mean: 35.868 Å2 / Biso min: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å2-1.15 Å2
2--1.25 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11296 0 166 234 11696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911676
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211282
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.97215736
X-RAY DIFFRACTIONr_angle_other_deg0.852326082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38751436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.6725.152528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.646152032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4091548
X-RAY DIFFRACTIONr_chiral_restr0.0880.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022516
X-RAY DIFFRACTIONr_mcbond_it2.3793.3835756
X-RAY DIFFRACTIONr_mcbond_other2.3793.3835755
X-RAY DIFFRACTIONr_mcangle_it3.7045.0687188
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 167 -
Rwork0.181 3303 -
all-3470 -
obs--98.36 %

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