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- PDB-3i4c: Crystal structure of Sulfolobus Solfataricus ADH(SsADH) double mu... -

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Basic information

Entry
Database: PDB / ID: 3i4c
TitleCrystal structure of Sulfolobus Solfataricus ADH(SsADH) double mutant (W95L,N249Y)
ComponentsNAD-dependent alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / ARCHAEON / ZINC / NAD(H)-DEPENDENT / MUTANT / Metal-binding / Methylation / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEsposito, L. / Pennacchio, A. / Zagari, A. / Rossi, M. / Raia, C.A.
CitationJournal: Extremophiles / Year: 2009
Title: Role of Tryptophan 95 in substrate specificity and structural stability of Sulfolobus solfataricus alcohol dehydrogenase
Authors: Pennacchio, A. / Esposito, L. / Zagari, A. / Rossi, M. / Raia, C.A.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 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

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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)226,33418
Polymers225,5496
Non-polymers78512
Water7,728429
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)150,88912
Polymers150,3664
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-33 kcal/mol
Surface area48050 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)150,88912
Polymers150,3664
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12360 Å2
ΔGint-29 kcal/mol
Surface area47080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.729, 91.545, 118.368
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NAD-dependent alcohol dehydrogenase


Mass: 37591.543 Da / Num. of mol.: 6 / Mutation: W95L, N249Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: adh, 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.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 7%(W/V) PEG 4000, 7%(V/V) ISOPROPANOL, 50MM SODIUM CITRATE PH 5.6, 50MM TRIS PH 7.8, 25MM COCL2 , VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 20, 2007 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 149954 / % possible obs: 97.8 % / Redundancy: 5 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.3 / Num. unique all: 13778 / % possible all: 90.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NTO

1nto


Resolution: 2→32.36 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 366826.86 / 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
Rfree0.25 7092 5 %RANDOM
Rwork0.228 ---
obs0.228 140498 91.5 %-
all-149954 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9411 Å2 / ksol: 0.373957 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å20 Å21.58 Å2
2--5.19 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 2→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14704 0 12 429 15145
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it3.162.5
X-RAY DIFFRACTIONc_scangle_it4.313
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 1040 5.1 %
Rwork0.269 19263 -
obs--79.8 %

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