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- PDB-1nto: N249Y MUTANT OF ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBU... -

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Basic information

Entry
Database: PDB / ID: 1nto
TitleN249Y MUTANT OF ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS-MONOCLINIC CRYSTAL FORM
ComponentsNAD-dependent alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / ARCHAEON / 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: 1.94 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: 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.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Three Dimensional Structure of Horse Liver Alcoholdehydrogenase 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
DepositionJan 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _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
B: NAD-dependent alcohol dehydrogenase
C: NAD-dependent alcohol dehydrogenase
D: NAD-dependent alcohol dehydrogenase
E: NAD-dependent alcohol dehydrogenase
H: NAD-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,77218
Polymers225,9886
Non-polymers78512
Water11,403633
1
A: NAD-dependent alcohol dehydrogenase
B: NAD-dependent alcohol dehydrogenase
C: NAD-dependent alcohol dehydrogenase
D: 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
Buried area12740 Å2
ΔGint-34 kcal/mol
Surface area48180 Å2
MethodPISA
2
E: NAD-dependent alcohol dehydrogenase
H: NAD-dependent alcohol dehydrogenase
hetero molecules

E: NAD-dependent alcohol dehydrogenase
H: 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 operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)215.327, 91.594, 118.238
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer. The asymmetric unit contains six monomers. Chains ABCD form a tetramer. The second tetramer is generated from chains EH in the asymmetric unit by the operation: -x+1, y, -z+1

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Components

#1: Protein
NAD-dependent alcohol dehydrogenase


Mass: 37664.594 Da / Num. of mol.: 6 / Mutation: N249Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ADH / 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.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.51 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 7%(w/v) PEG 4000, 7%(v/v) Isopropanol, 50 mM Sodium citrate pH 5.6, 50 mM Tris pH 7.8 , 25 mM CoCl2 , VAPOR DIFFUSION, HANGING DROP, 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: ELETTRA / Beamline: 5.2R / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→15 Å / Num. obs: 146709 / % possible obs: 87.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.8
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 11.7 / % possible all: 86.9
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 554277
Reflection shell
*PLUS
% possible obs: 86.9 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 12

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Processing

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

1jvb


Resolution: 1.94→15 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 7341 5.1 %RANDOM
Rwork0.21 ---
all0.214 146709 --
obs0.211 145308 86.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.59 Å2 / ksol: 0.4714 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å22.27 Å2
2--2.46 Å20 Å2
3----0.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.94→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15709 0 12 633 16354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 1.94→2.01 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.281 693 5.1 %
Rwork0.226 13005 -
obs-13698 82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3WATER.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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