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

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Basic information

Entry
Database: PDB / ID: 7ude
TitleHorse liver alcohol dehydrogenase with NAD and trifluoroethanol at 125 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 / 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 18, 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
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-113 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.280, 51.180, 92.590
Angle α, β, γ (deg.)91.900, 103.020, 109.890
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 / 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

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 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→19.97 Å / Num. obs: 282985 / % possible obs: 94.2 % / Redundancy: 4.01 % / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.059 / Χ2: 1.19 / Net I/σ(I): 8.9 / Num. measured all: 1144666 / Scaling rejects: 8585
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.1-1.144.020.5311.3111117274430.6121.8681291.2
1.14-1.184.040.4351.9111940275680.5021.6957891.8
1.18-1.244.030.3482.5112202277130.4011.5346792.5
1.24-1.34.030.2793.2113522280710.3211.3941893.2
1.3-1.394.030.2074.3114007281800.2391.2438793.9
1.39-1.494.030.1515.7114940283900.1751.0654494.7
1.49-1.644.030.1047.5116506286820.120.8984195.5
1.64-1.884.020.0710.5117227288600.0810.75130096.2
1.88-2.373.910.0418.9115474291960.0470.72135497.2
2.37-19.974.010.02832.7117731288820.0320.81188496.2

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8Ldata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
d*TREKdata reduction
Omodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ua6

7ua6


Resolution: 1.1→19.97 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.043 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1599 2759 1 %RANDOM
Rwork0.1334 ---
obs0.1337 278692 93.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.61 Å2 / Biso mean: 15.398 Å2 / Biso min: 7.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.02 Å2
2--0.05 Å2-0.04 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.1→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 144 904 6618
Biso mean--17.88 27.66 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176107
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.6878499
X-RAY DIFFRACTIONr_angle_other_deg1.5471.59214252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03523.099242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.874151143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5911526
X-RAY DIFFRACTIONr_chiral_restr0.1170.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021222
X-RAY DIFFRACTIONr_rigid_bond_restr2.865312341
LS refinement shellResolution: 1.1→1.128 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 184 -
Rwork0.36 19549 -
all-19733 -
obs--88.9 %

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