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- PDB-3rj5: Structure of alcohol dehydrogenase from Drosophila lebanonesis T1... -

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Basic information

Entry
Database: PDB / ID: 3rj5
TitleStructure of alcohol dehydrogenase from Drosophila lebanonesis T114V mutant complexed with NAD+
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenases/reductases / detoxification / NAD metabolism
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / identical protein binding / cytoplasm
Similarity search - Function
Alcohol dehydrogenase, Drosophila-type / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesScaptodrosophila lebanonensis (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMorgunova, E. / Wuxiuer, Y. / Cols, N. / Popov, A. / Sylte, I. / Karshikoff, A. / Gonzales-Duarte, R. / Ladenstein, R. / Winberg, J.O.
CitationJournal: Febs J. / Year: 2012
Title: An intact eight-membered water chain in drosophilid alcohol dehydrogenases is essential for optimal enzyme activity.
Authors: Wuxiuer, Y. / Morgunova, E. / Cols, N. / Popov, A. / Karshikoff, A. / Sylte, I. / Gonzalez-Duarte, R. / Ladenstein, R. / Winberg, J.O.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Aug 8, 2012Group: Database references
Revision 1.3Sep 13, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3674
Polymers55,6442
Non-polymers7232
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-45 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.300, 53.870, 76.750
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alcohol dehydrogenase


Mass: 27822.000 Da / Num. of mol.: 2 / Mutation: T114V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scaptodrosophila lebanonensis (fry) / Gene: Adh / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM205 / References: UniProt: P10807, alcohol dehydrogenase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24.8% PEG (3350), 0.2M lithium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97245 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2008 / Details: bent cylindrical mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97245 Å / Relative weight: 1
ReflectionResolution: 1.45→31.25 Å / Num. obs: 103038 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.4
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.2 / Num. unique all: 13812 / % possible all: 90.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1a4u

1a4u


Resolution: 1.45→31.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.318 / SU ML: 0.071 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23921 2047 2 %RANDOM
Rwork0.20584 ---
obs0.2065 100725 97.76 %-
all-103038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.148 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-0.15 Å2
2--2.67 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 48 594 4534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224156
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9635693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4525538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20725.145173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.415718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5421517
X-RAY DIFFRACTIONr_chiral_restr0.080.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023076
X-RAY DIFFRACTIONr_nbd_refined0.1990.22179
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2487
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.233
X-RAY DIFFRACTIONr_mcbond_it0.6641.52653
X-RAY DIFFRACTIONr_mcangle_it1.03724200
X-RAY DIFFRACTIONr_scbond_it1.43231711
X-RAY DIFFRACTIONr_scangle_it2.1494.51475
X-RAY DIFFRACTIONr_rigid_bond_restr0.79334364
X-RAY DIFFRACTIONr_sphericity_free2.8153594
X-RAY DIFFRACTIONr_sphericity_bonded2.10634059
LS refinement shellResolution: 1.449→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 130 -
Rwork0.371 6037 -
obs-100725 80.64 %

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