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- PDB-1r37: Alcohol dehydrogenase from sulfolobus solfataricus complexed with... -

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Basic information

Entry
Database: PDB / ID: 1r37
TitleAlcohol dehydrogenase from sulfolobus solfataricus complexed with NAD(H) and 2-ethoxyethanol
ComponentsNAD-dependent alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / archaeon / zinc / NAD(H) dependent / holoform
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / 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
2-ETHOXYETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent alcohol dehydrogenase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEsposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal structure of a ternary complex of the alcohol dehydrogenase from Sulfolobus solfataricus
Authors: Esposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the alcohol dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus at 1.85 A resolution
Authors: Esposito, L. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
#2: Journal: FEBS Lett. / Year: 2003
Title: Structural study of a single-point mutant of Sulfolobus solfataricus alcohol dehydrogenase with enhanced activity
Authors: Esposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
History
DepositionSep 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent alcohol dehydrogenase
B: NAD-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,00010
Polymers75,2312
Non-polymers1,7698
Water3,675204
1
A: NAD-dependent alcohol dehydrogenase
B: NAD-dependent alcohol dehydrogenase
hetero molecules

A: NAD-dependent alcohol dehydrogenase
B: NAD-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,00020
Polymers150,4624
Non-polymers3,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)131.064, 83.014, 68.674
Angle α, β, γ (deg.)90.00, 96.46, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -x+1, y, -z+1

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Components

#1: Protein NAD-dependent alcohol dehydrogenase


Mass: 37615.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HOLO-ENZYME FORM / Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ADH or SSO2536 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): RB791 / References: UniProt: P39462, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 40%(V/V) 2-ethoxyethanol, 100MM NA/K phosphate, 200MM NACL, 2MM NAD+(NADH), pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
22 mMNAD+1drop
310 mM2,2,2-trifluoroethanol1drop
4100 mMsodium/pootassium phosphate1reservoirpH6.2
5200 mM1reservoirNaCl
640 %(v/v)2-ethoxyethanol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 29287 / Num. obs: 29287 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 8.8 / Num. unique all: 1962 / % possible all: 60.8
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Num. measured all: 70105
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 60.8 % / Mean I/σ(I) obs: 8.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JVB

1jvb


Resolution: 2.3→25 Å / Rfactor Rfree error: 0.006 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: This C2 crystal displays non-merohedral twinning. the two reciprocal lattices are related by a 180 degree rotation about the A axis. Spots from the dominant lattice (~70%) were indexed and ...Details: This C2 crystal displays non-merohedral twinning. the two reciprocal lattices are related by a 180 degree rotation about the A axis. Spots from the dominant lattice (~70%) were indexed and reduced; this dataset was used for the structure refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1521 5.2 %RANDOM
Rwork0.193 ---
all0.195 29220 --
obs-29131 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.14 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.72 Å20 Å21.18 Å2
2---5.11 Å20 Å2
3---10.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 104 204 5584
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.268 110 5.8 %
Rwork0.183 1849 -
obs-1937 61 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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