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- PDB-1jvb: ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS -

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Basic information

Entry
Database: PDB / ID: 1jvb
TitleALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS
ComponentsNAD(H)-DEPENDENT ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ARCHAEON / ZINC / NAD
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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...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 / Polyketide synthase, enoylreductase domain / Enoylreductase / 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
NAD-dependent alcohol dehydrogenase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsEsposito, L. / Sica, F. / Zagari, A. / Mazzarella, L.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: NADP-dependent Bacterial Alcohol Dehydrogenases: Crystal Structure, Co-Factor-Binding and Co-Factor Specificity of the ADHS of Clostridium beijerinckii and Thermoanaerobacter brockii
Authors: Korkhin, Y. / Kalb, A.J. / Peretz, M. / Bogin, O. / Burstein, Y. / Frolow, F.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of NADP(H)-Dependent Ketose Reductase from Besimia Argentifolii at 2.3 Angstrom Resolution
Authors: Banfield, M.J. / Salvucci, M.E. / Baker, E.N. / Smith, C.A.
History
DepositionAug 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(H)-DEPENDENT ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1213
Polymers37,9911
Non-polymers1312
Water3,477193
1
A: NAD(H)-DEPENDENT ALCOHOL DEHYDROGENASE
hetero molecules

A: NAD(H)-DEPENDENT ALCOHOL DEHYDROGENASE
hetero molecules

A: NAD(H)-DEPENDENT ALCOHOL DEHYDROGENASE
hetero molecules

A: NAD(H)-DEPENDENT ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,48612
Polymers151,9634
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Unit cell
Length a, b, c (Å)125.316, 125.316, 115.590
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 the monomer in the asymmetric unit by the operations: -y,-x,-z, y,x,-z, -x,-y,z

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Components

#1: Protein NAD(H)-DEPENDENT ALCOHOL DEHYDROGENASE


Mass: 37990.680 Da / Num. of mol.: 1 / Fragment: APO-ENZYME FORM
Source method: isolated from a genetically manipulated source
Details: APO-ENZYME FORM / Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ADH / 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


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 295 K / Method: batch / pH: 6.3
Details: 6% (V/V) PEG 4000, 6% (V/V) ISOPROPANOL, 50MM SODIUM CITRATE PH 5.6, 50MM TRIS PH 7.8, pH 6.3, batch, temperature 295K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124 mg/mlprotein1drop
2100 mMTris-HCl1droppH7.8
310 mMdithiothreitol1drop
412 %(w/v)PEG40001reservoir
512 %(v/v)2-propanol1reservoir
6100 mMsodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9830, 0.9795, 0.9792, 0.9537
DetectorType: ADSC / Detector: CCD / Date: Nov 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9831
20.97951
30.97921
40.95371
ReflectionResolution: 1.85→40 Å / Num. all: 39211 / Num. obs: 39211 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 37.8
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 6.3 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 393222 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.358

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Processing

Software
NameVersionClassification
SOLVEphasing
DMmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→40 Å / Rfactor Rfree error: 0.004 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3816 10 %RANDOM
Rwork0.191 ---
all-39211 --
obs-38129 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.61 Å2 / ksol: 0.352225 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 2 193 2816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 1.85→1.89 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.272 215 9.6 %
Rwork0.234 2013 -
obs--85.3 %
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.272 / Rfactor Rwork: 0.234

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