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- PDB-7uc9: Horse liver alcohol dehydrogenase with NAD and trifluoroethanol a... -

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Basic information

Entry
Database: PDB / ID: 7uc9
TitleHorse liver alcohol dehydrogenase with NAD and trifluoroethanol at 45 K
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase liver / METAL BINDING PROTEIN
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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 ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIFLUOROETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsPlapp, B.V. / Gakhar, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AA00279 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM078446 United States
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2022
Title: Dependence of crystallographic atomic displacement factors on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenases
Authors: Plapp, B.V. / Gakhar, L. / Subramanian, R.
#1: Journal: Biochemistry / Year: 2012
Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes.
Authors: Plapp, B.V. / Ramaswamy, S.
History
DepositionMar 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references
Category: citation / citation_author / pdbx_related_exp_data_set
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,96814
Polymers79,7072
Non-polymers2,26112
Water15,763875
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-113 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.190, 51.120, 92.460
Angle α, β, γ (deg.)91.900, 103.030, 109.800
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: liver / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 887 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ETF / TRIFLUOROETHANOL


Mass: 100.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3F3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: block
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 100 MM 2,2,2-TRIFLUOROETHANOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Temp details: pH 6.7 at 298 K

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Data collection

DiffractionMean temperature: 45 K / Ambient temp details: He cryostat / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2009
Details: ROSENBAUM ROCK VERTICAL FOCUSINGMIRROR WITH PT, GLASS, PD LANES
RadiationMonochromator: ROSENBAUM ROCK HIGH RESOLUTION DOUBLE CRYSTAL MONOCHROMATOR, LN2 COOLED, SAGITTAL FOCUSSING 2ND MIRROR, SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→19.94 Å / Num. obs: 281686 / % possible obs: 93.6 % / Redundancy: 3.78 % / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.059 / Χ2: 1.18 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
1.1-1.143.780.4092.2260950.4761.886.6
1.14-1.183.810.3322.7275350.3861.6291.7
1.18-1.243.80.2653.4277460.3081.4992.3
1.24-1.33.790.2174.2280370.2521.3693
1.3-1.383.790.1665.2282240.1931.1993.8
1.38-1.493.80.1266.4284400.1471.0394.6
1.49-1.643.810.0918.5286700.1060.8995.4
1.64-1.883.810.06611.6289260.0760.7996.2
1.88-2.363.70.0420.4292670.0460.8397.2
2.36-19.943.750.03132.2287460.0360.9395.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
d*TREKdata reduction
d*TREK9.9.9.8Ldata scaling
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7au6

7au6


Resolution: 1.1→19.94 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.935 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.152 2760 1 %RANDOM
Rwork0.1261 ---
obs0.1263 277899 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.31 Å2 / Biso mean: 14.587 Å2 / Biso min: 6.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0.25 Å20.19 Å2
2--0.31 Å20.21 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.1→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 144 904 6618
Biso mean--17.1 26.39 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176107
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.6878499
X-RAY DIFFRACTIONr_angle_other_deg1.551.59214252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6545806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98323.099242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.942151143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2471526
X-RAY DIFFRACTIONr_chiral_restr0.1110.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021222
X-RAY DIFFRACTIONr_rigid_bond_restr2.661312341
LS refinement shellResolution: 1.1→1.128 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 192 -
Rwork0.273 19682 -
all-19874 -
obs--89.93 %

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