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- PDB-1nvg: N249Y MUTANT OF THE ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFO... -

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Basic information

Entry
Database: PDB / ID: 1nvg
TitleN249Y MUTANT OF THE ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS-TETRAGONAL CRYSTAL FORM
ComponentsNAD-dependent alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / ARCHAEON / ZINC / NAD(H) dependent / mutant
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
NAD-dependent alcohol dehydrogenase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEsposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Sulfolobus Solfataricus at 1.85 Angstrom Resolution
Authors: Esposito, L. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
#2: Journal: Biochemistry / Year: 1999
Title: Asn249Tyr Substitution at the Coenzyme Binding Domain Activates Sulfolobus Solfataricus Alcohol Dehydrogenase and Increases its Thermal Stability
Authors: Giordano, A. / Cannio, R. / La Cara, F. / Bartolucci, S. / Rossi, M. / Raia, C.A.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Three Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstrom Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A.
History
DepositionFeb 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7953
Polymers37,6651
Non-polymers1312
Water2,162120
1
A: NAD-dependent alcohol dehydrogenase
hetero molecules

A: NAD-dependent alcohol dehydrogenase
hetero molecules

A: NAD-dependent alcohol dehydrogenase
hetero molecules

A: NAD-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,18212
Polymers150,6584
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation15_555y,x,-z1
crystal symmetry operation10_555-x,-y,z1
Unit cell
Length a, b, c (Å)125.396, 125.396, 117.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a tetramer generated from chain A in the asymmetric unit by the following symmetry operations: -y,-x,-z; y,x,-z; -x,-y, z.

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Components

#1: Protein NAD-dependent alcohol dehydrogenase


Mass: 37664.594 Da / Num. of mol.: 1 / Mutation: N249Y
Source method: isolated from a genetically manipulated source
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 296 K / Method: batch
Details: 7% (W/V) PEG 4000, 7% (V/V) ISOPROPANOL, 50mM SODIUM CITRATE PH 5.6, 50mM TRIS PH 7.8, pH NULL, BATCH, temperature 296K
Crystal grow
*PLUS
Details: Pearl, L., (1993) J. Mol. Biol., 229, 782.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 / Wavelength: 0.9393 Å
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: 2.5→25 Å / Num. all: 15757 / Num. obs: 15757 / % possible obs: 95 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 32.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 16.3 / Num. unique all: 1584 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. measured all: 104158
Reflection shell
*PLUS
% possible obs: 96.9 % / Mean I/σ(I) obs: 16

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Processing

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

1nto


Resolution: 2.5→25 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1230 7.9 %RANDOM
Rwork0.196 ---
all0.203 ---
obs0.196 15490 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å20 Å20 Å2
2--2.86 Å20 Å2
3----5.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 2 120 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.962.5
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 121 7.9 %
Rwork0.26 1411 -
obs-1532 94.6 %
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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