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- PDB-1y9a: Alcohol Dehydrogenase from Entamoeba histolotica in complex with ... -

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Basic information

Entry
Database: PDB / ID: 1y9a
TitleAlcohol Dehydrogenase from Entamoeba histolotica in complex with cacodylate
ComponentsNADP-dependent alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Metal-binding / NADP
Function / homology
Function and homology information


isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding / cytoplasm
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
ACETATE ION / CACODYLATE ION / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsShimon, L.J. / Peretz, M. / Goihberg, E. / Burstein, Y. / Frolow, F.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of alcohol dehydrogenase from Entamoeba histolytica.
Authors: Shimon, L.J. / Goihberg, E. / Peretz, M. / Burstein, Y. / Frolow, F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Thermophilic alcohol dehydrogenase from the mesophile Entamoeba histolytica: crystallization and preliminary
Authors: Shimon, L.J.W. / Peretz, M. / Goihberg, E. / Burstein, Y. / Frolow, F.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent alcohol dehydrogenase
C: NADP-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,40817
Polymers77,3952
Non-polymers1,01315
Water13,583754
1
A: NADP-dependent alcohol dehydrogenase
C: NADP-dependent alcohol dehydrogenase
hetero molecules

A: NADP-dependent alcohol dehydrogenase
C: NADP-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,81634
Polymers154,7914
Non-polymers2,02530
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area18690 Å2
ΔGint-241 kcal/mol
Surface area46270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.891, 234.139, 96.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2002-

ZN

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein NADP-dependent alcohol dehydrogenase


Mass: 38697.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: ADH1 / Plasmid: bs-p58 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-I / References: UniProt: P35630, alcohol dehydrogenase (NADP+)

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Non-polymers , 6 types, 769 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.77 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000 14%w/v, 300 mM Mg Acetate, 200mM cacodylate at pH 6.5, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 74221 / Rmerge(I) obs: 0.056
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.830.486196.3
1.83-1.860.386196.8
1.86-1.90.335196.5
1.9-1.940.287196
1.94-1.980.24195.8
1.98-2.030.182195.7
2.03-2.080.165195.2
2.08-2.130.136195
2.13-2.20.12194.1
2.2-2.270.105193.7
2.27-2.350.092193.4
2.35-2.440.083192.7
2.44-2.550.074192.2
2.55-2.690.072192.5
2.69-2.860.056192.1
2.86-3.070.049191.8
3.07-3.380.043191.3
3.38-3.870.034189.9
3.87-4.860.028188.1
4.86-200.029182.1

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Phasing

Phasing MRRfactor: 0.477 / Cor.coef. Fo:Fc: 0.444
Highest resolutionLowest resolution
Rotation3 Å19.95 Å
Translation3 Å19.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.401data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→117.04 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.781 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17707 3722 5 %RANDOM
Rwork0.12625 ---
obs0.12885 70422 92.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.091 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20 Å2
2--2.16 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.81→117.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 44 754 6216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225566
X-RAY DIFFRACTIONr_bond_other_d0.0010.025199
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9747493
X-RAY DIFFRACTIONr_angle_other_deg0.868312105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61224.434212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44115967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8671526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021020
X-RAY DIFFRACTIONr_nbd_refined0.2180.21098
X-RAY DIFFRACTIONr_nbd_other0.1860.25467
X-RAY DIFFRACTIONr_nbtor_refined0.170.22661
X-RAY DIFFRACTIONr_nbtor_other0.0850.23225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2544
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0840.21
X-RAY DIFFRACTIONr_metal_ion_refined0.150.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.256
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.2143
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1570.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other0.2
X-RAY DIFFRACTIONr_mcbond_it2.78934510
X-RAY DIFFRACTIONr_mcbond_other1.22631506
X-RAY DIFFRACTIONr_mcangle_it3.46755668
X-RAY DIFFRACTIONr_scbond_it4.73172281
X-RAY DIFFRACTIONr_scangle_it6.108101825
X-RAY DIFFRACTIONr_rigid_bond_restr2.212312609
X-RAY DIFFRACTIONr_sphericity_free6.6893756
X-RAY DIFFRACTIONr_sphericity_bonded2.916310661
LS refinement shellResolution: 1.81→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 248 -
Rwork0.157 5252 -
obs--93.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.24410.03180.0370.13740.02650.4-0.0004-0.0855-0.05110.01490.02940.02950.0802-0.0232-0.0290.0427-0.00550.0019-0.02020.0305-0.0383-7.23772.33743.887
20.44410.0220.06940.0649-0.01480.1061-0.0057-0.01890.122-0.00310.0261-0.02170.01610.0284-0.0204-0.00710.0023-0.0036-0.0447-0.02820.025220.34399.12329.77
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3601 - 360
2X-RAY DIFFRACTION2CB1 - 3601 - 360

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