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- PDB-3wie: Structure of a glucose dehydrogenase T277F mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 3wie
TitleStructure of a glucose dehydrogenase T277F mutant in complex with D-glucose and NAADP
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
beta-D-glucopyranose / Chem-DN4 / Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Dec 25, 2019Group: Data collection / Database references / Category: chem_comp / citation / struct_ref_seq_dif
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)169,87820
Polymers165,6564
Non-polymers4,22116
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15090 Å2
ΔGint-212 kcal/mol
Surface area52100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.910, 92.331, 120.470
Angle α, β, γ (deg.)90.00, 91.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41414.113 Da / Num. of mol.: 4 / Mutation: T277F
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-DN4 / [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(3-carboxypyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate / Nicotinic acid adenine dinucleotide phosphate


Mass: 744.390 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N6O18P3
#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, 1,2-propanediol, HEPES, NAADP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 24, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. all: 75199 / Num. obs: 75199 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.33→2.37 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
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wid

3wid


Resolution: 2.33→28.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.634 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.317 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 3752 5 %RANDOM
Rwork0.1909 ---
all0.1936 75199 --
obs0.1936 74890 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.12 Å2 / Biso mean: 49.6365 Å2 / Biso min: 19.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å2-0.14 Å2
2--2.42 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.33→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11308 0 248 216 11772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211809
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211204
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.98816014
X-RAY DIFFRACTIONr_angle_other_deg0.9343.00725896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03451436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11225.113532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.442152032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6151548
X-RAY DIFFRACTIONr_chiral_restr0.1090.21784
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022568
X-RAY DIFFRACTIONr_mcbond_it4.0344.6435756
X-RAY DIFFRACTIONr_mcbond_other4.0344.6435755
X-RAY DIFFRACTIONr_mcangle_it5.6996.9527188
LS refinement shellResolution: 2.329→2.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 288 -
Rwork0.232 5032 -
all-5320 -
obs--95.1 %

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