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

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Basic information

Entry
Database: PDB / ID: 2cdc
TitleSulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP and Xylose
ComponentsGLUCOSE DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1
KeywordsOXIDOREDUCTASE / GLUCOSE DEHYDROGENASE / 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(P)+] 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(P)+] activity / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / 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 ...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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / beta-D-xylopyranose / alpha-D-xylopyranose / Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 28, 2018Group: Atomic model / Database references / Source and taxonomy
Category: atom_site / citation / entity_src_gen
Item: _atom_site.occupancy / _citation.journal_abbrev ..._atom_site.occupancy / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 / _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 3.1Dec 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
Revision 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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 DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1
B: GLUCOSE DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1
C: GLUCOSE DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1
D: GLUCOSE DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,84529
Polymers163,6614
Non-polymers5,18425
Water28,4641580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.644, 91.032, 138.725
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GLUCOSE DEHYDROGENASE GLUCOSE 1-DEHYDROGENASE, DHG-1


Mass: 40915.254 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET3A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O93715, glucose 1-dehydrogenase [NAD(P)+]

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Sugars , 2 types, 10 molecules

#3: Sugar
ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1595 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1580 / 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
Has protein modificationY
Sequence detailsMUTATION OF THR41 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: 2.27 Å3/Da / Density % sol: 45.34 %
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: 1.5→41.2 Å / Num. obs: 191673 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.5 / % possible all: 80.1

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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: 1.5→138.68 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.376 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / 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 AND OCCUPANCY OF 0.01
RfactorNum. reflection% reflectionSelection details
Rfree0.239 12721 5 %RANDOM
Rwork0.204 ---
obs0.206 240504 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.64 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.5→138.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11288 0 312 1580 13180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.325216681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66851470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1624.763527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.227152261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3521566
X-RAY DIFFRACTIONr_chiral_restr0.0880.21936
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.26592
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.28277
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.21436
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6961.57529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.085211934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.62335414
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4024.54747
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 700
Rwork0.269 14062

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