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- PDB-2cda: Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP -

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Basic information

Entry
Database: PDB / ID: 2cda
TitleSulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP
ComponentsGLUCOSE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / GLUCOSE DEHYDROGENASE / MEDIUM CHAIN DEHYDROGENASE 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,6398
Polymers81,8912
Non-polymers1,7486
Water2,810156
1
A: GLUCOSE DEHYDROGENASE
B: GLUCOSE DEHYDROGENASE
hetero molecules

A: GLUCOSE DEHYDROGENASE
B: GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,27816
Polymers163,7814
Non-polymers3,49712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.620, 92.296, 138.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 40945.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PREC7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): JM109
References: UniProt: O93715, glucose 1-dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.7 Å3/Da / Density % sol: 57.4 %
Crystal growDetails: 8 % PEG 8000, 0.1 MM TRIS (PH 8.0), 4.5 % PROPAN-2-OL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.28→51.2 Å / Num. obs: 38690 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.8
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.3 / % possible all: 99.6

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Processing

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

2cd9


Resolution: 2.28→138.68 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.883 / SU B: 8.894 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOP REGION IS DELETED FROM THE COORDINATES
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2008 5 %RANDOM
Rwork0.196 ---
obs0.198 38076 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--1.6 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.28→138.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 0 100 156 5913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225869
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9927951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5315715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14824.715246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.962151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8551530
X-RAY DIFFRACTIONr_chiral_restr0.1230.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024286
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23930
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2311
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.2105
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0341.53680
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68825758
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.51232541
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7824.52193
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: 2.28→2.34 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 153
Rwork0.24 2819

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