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- PDB-2cdb: Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with N... -

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Basic information

Entry
Database: PDB / ID: 2cdb
TitleSulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP and glucose
ComponentsGLUCOSE 1-DEHYDROGENASE (DHG-1)
KeywordsOXIDOREDUCTASE / REDUCTASE / MDR FAMILY
Function / homology
Function and homology information


aldose 1-dehydrogenase [NAD(P)+] / xylose binding / galactose catabolic process via D-galactonate / aldose 1-dehydrogenase activity / galactose 1-dehydrogenase (NADP+) / galactose 1-dehydrogenase (NADP+) activity / D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / non-phosphorylated glucose catabolic process / glucose 1-dehydrogenase (NAD+) activity ...aldose 1-dehydrogenase [NAD(P)+] / xylose binding / galactose catabolic process via D-galactonate / aldose 1-dehydrogenase activity / galactose 1-dehydrogenase (NADP+) / galactose 1-dehydrogenase (NADP+) activity / D-galactose 1-dehydrogenase / galactose 1-dehydrogenase activity / non-phosphorylated glucose catabolic process / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / galactose binding / D-glucose binding / NADP+ binding / NAD+ binding / protein tetramerization / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMilburn, C.C. / Lamble, H.J. / Theodossis, A. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Structural Basis of Substrate Promiscuity in Glucose Dehydrogenase from the Hyperthermophilic Archaeon Sulfolobus Solfataricus.
Authors: Milburn, C.C. / Lamble, H.J. / Theodossis, A. / Bull, S.D. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
History
DepositionJan 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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 / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2 / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSE 1-DEHYDROGENASE (DHG-1)
B: GLUCOSE 1-DEHYDROGENASE (DHG-1)
C: GLUCOSE 1-DEHYDROGENASE (DHG-1)
D: GLUCOSE 1-DEHYDROGENASE (DHG-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,12724
Polymers163,6614
Non-polymers4,46620
Water22,9871276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21950 Å2
ΔGint-195 kcal/mol
Surface area49460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.672, 91.394, 138.433
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
GLUCOSE 1-DEHYDROGENASE (DHG-1) / DHG-1 / GLUCOSE DEHYDROGENASE


Mass: 40915.254 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O93715, glucose 1-dehydrogenase [NAD(P)+]
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / 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

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Non-polymers , 4 types, 1292 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1276 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 41 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 41 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, THR 41 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 41 TO ALA ENGINEERED RESIDUE IN CHAIN C, THR 41 TO ALA ENGINEERED RESIDUE IN CHAIN D, THR 41 TO ALA
Sequence detailsMUTATED THR 41 TO ALA

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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: 2.36 Å3/Da / Density % sol: 47.55 %
Crystal growDetails: 8 % PEG 8000, 0.1 M TRIS (PH 8.0), 4.5 % (V/V) PROPAN-2-OL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→41.2 Å / Num. obs: 203195 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.1 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CD9

2cd9


Resolution: 1.6→138.68 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.499 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOP REGIONS ARE DELETED FROM PDB FILE. DISORDERED SIDECHAINS ARE INDICATED BY AN OCCUPANCY OF 0.01.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 10908 5.08 %RANDOM
Rwork0.19 ---
obs0.192 216944 96.4 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.057 Å20 Å20 Å2
2--0.831 Å20 Å2
3----0.774 Å2
Refinement stepCycle: LAST / Resolution: 1.6→138.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11293 0 264 1276 12833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.99716377
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75151447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32724.837521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.121152224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8261564
X-RAY DIFFRACTIONr_chiral_restr0.0870.21894
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.26243
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.28211
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.21222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.57422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.078211756
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74535286
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6224.54621
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 7.15→138.68 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 111
Rwork0.209 2234
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.44770.16010.09690.8240.10370.35120.0167-0.0378-0.03610.09880.0016-0.07380.05610.0304-0.0182-0.00190.0053-0.0144-0.0110.0084-0.02957.2688.074-12.758
20.3879-0.0053-0.00790.7721-0.18070.5516-0.01290.0693-0.0258-0.1270.02340.060.0717-0.023-0.01040.0003-0.003-0.01780.0069-0.018-0.032844.28210.198-57.332
30.57660.1305-0.10690.30820.03240.2828-0.00030.0063-0.01390.0197-0.01270.05190.0516-0.04180.013-0.0089-0.01460.0074-0.0226-0.0013-0.019335.2562.064-22.997
4000000000000000000000000
50.38860.05440.06830.6216-0.10970.5287-0.018-0.03550.02960.11060.02530.0497-0.0508-0.0477-0.0072-0.00150.01080.0159-0.0089-0.0134-0.03345.6336.259-11.869
60.3874-0.0546-0.02790.85630.07680.49780.00270.0610.0185-0.13960.0179-0.0719-0.06940.0123-0.02050.0054-0.00130.02640.00990.0165-0.036858.86136.968-56.363
70.6376-0.00310.14810.3339-0.01240.293-0.02130.0080.04490.03610.0124-0.0897-0.0420.03840.0089-0.0156-0.0126-0.0142-0.0214-0.0062-0.00567.46642.927-21.889
80.4247-0.17080.10110.44730.00370.3816-0.00030.01410.0045-0.04570.00660.0659-0.0752-0.059-0.0062-0.00610.0223-0.0074-0.0110.0152-0.018237.55545.124-46.073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 300
2X-RAY DIFFRACTION2B187 - 300
3X-RAY DIFFRACTION3A1 - 186
4X-RAY DIFFRACTION3A301 - 366
5X-RAY DIFFRACTION4B1 - 186
6X-RAY DIFFRACTION4B301 - 366
7X-RAY DIFFRACTION5C187 - 300
8X-RAY DIFFRACTION6D187 - 300
9X-RAY DIFFRACTION7C1 - 186
10X-RAY DIFFRACTION7C301 - 366
11X-RAY DIFFRACTION8D1 - 186
12X-RAY DIFFRACTION8D301 - 366

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