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- PDB-7uej: horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl ... -

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Basic information

Entry
Database: PDB / ID: 7uej
Titlehorse liver alcohol dehydrogenase with NAD and pentafluorobenzyl alcohol at 150 K
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase NAD pentafluorobenzyl alcohol horse liver 150 K
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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPlapp, B.V. / Gakhar, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)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 21, 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.title / _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)82,16414
Polymers79,7072
Non-polymers2,45712
Water14,952830
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-106 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.380, 51.330, 92.630
Angle α, β, γ (deg.)91.860, 103.050, 110.140
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, 842 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#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-PFB / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL


Mass: 198.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H3F5O / 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.: 830 / 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: 2.26 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+, 10 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 150 K / Ambient temp details: N2 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 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: 1.2→19.62 Å / Num. obs: 220796 / % possible obs: 95.1 % / Redundancy: 4.05 % / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.066 / Χ2: 1.2 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.2-1.244.090.568188013214210.6541.8741392.5
1.24-1.294.10.491.388861216130.5641.7331593.1
1.29-1.354.10.388289613217940.4461.5723993.7
1.35-1.424.090.2972.889773218750.3411.3928594.3
1.42-1.514.090.2183.990452220230.2521.2439194.9
1.51-1.634.060.1465.690580221280.1691.0668895.4
1.63-1.794.040.1037.491114223240.1190.8999796.1
1.79-2.0540.06910.991121224630.080.76123796.7
2.05-2.583.910.04417.689444226230.0510.7494297.6
2.58-19.614.070.0352692905225320.0410.81125897

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7udr

7udr


Resolution: 1.2→19.62 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.39 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1535 2159 1 %RANDOM
Rwork0.1285 ---
obs0.1287 216583 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.88 Å2 / Biso mean: 16.762 Å2 / Biso min: 7.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0.4 Å20.36 Å2
2--0.24 Å20.14 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 1.2→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 158 855 6583
Biso mean--18.75 29.94 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0136277
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156159
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.6868563
X-RAY DIFFRACTIONr_angle_other_deg1.561.59214391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27923.208240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.292151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0621525
X-RAY DIFFRACTIONr_chiral_restr0.1250.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026869
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021227
X-RAY DIFFRACTIONr_rigid_bond_restr3.695312436
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 152 -
Rwork0.323 15141 -
all-15293 -
obs--89.26 %

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