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- PDB-6xt2: EQADH-NADH-HEPTAFLUOROBUTANOL, P21 -

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Basic information

Entry
Database: PDB / ID: 6xt2
TitleEQADH-NADH-HEPTAFLUOROBUTANOL, P21
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / NADH / horse liver
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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 domain superfamily
Similarity search - Domain/homology
2,2,3,3,4,4,4-heptafluorobutan-1-ol / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPlapp, B.V. / Ramaswamy, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
Citation
Journal: Arch.Biochem.Biophys. / Year: 2021
Title: Alternative binding modes in abortive NADH-alcohol complexes of horse liver alcohol dehydrogenase.
Authors: Plapp, B.V. / 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.
#2: Journal: Biochemistry / Year: 2017
Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.
Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,63522
Polymers159,4134
Non-polymers4,22218
Water21,9601219
1
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,81711
Polymers79,7072
Non-polymers2,1119
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-58 kcal/mol
Surface area27230 Å2
MethodPISA
2
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,81711
Polymers79,7072
Non-polymers2,1119
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-57 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.150, 180.270, 86.900
Angle α, β, γ (deg.)90.000, 105.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1237 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-B7F / 2,2,3,3,4,4,4-heptafluorobutan-1-ol


Mass: 200.055 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3F7O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1219 / 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: 2.24 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 10 mg/ml protein, 1 mM NAD+, 4 mM 1H,1H-heptafluorobutanol, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethananesulfonate, 10-25% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: AREA DETECTOR / Date: Apr 12, 2004 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→19.92 Å / Num. obs: 188871 / % possible obs: 88.3 % / Redundancy: 5.64 % / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.053 / Χ2: 1.13 / Net I/σ(I): 20.7 / Num. measured all: 1072997 / Scaling rejects: 8048
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.55-1.612.620.2793.143116164360.3460.99577.2
1.61-1.673.240.2423.656636174820.2860.94181.5
1.67-1.753.340.2064.159890179200.2430.94284.3
1.75-1.843.760.1735.169057183830.20.99186.2
1.84-1.954.390.1516.582660188020.171.095188.1
1.95-2.15.860.1269.5111895190610.1381.224389.1
2.1-2.316.340.09912.5119199187110.1071.1655987.6
2.31-2.656.590.07516.5128708194010.0811.0684990.5
2.65-3.337.840.05125.3167530211920.0541.03147898.9
3.33-19.9210.680.03351.3234306214830.0351.32485999.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
d*TREK9.9.9.8Ldata scaling
PDB_EXTRACT3.25data extraction
d*TREKdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VL0

5vl0


Resolution: 1.55→19.84 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.501 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1923 1769 0.9 %RANDOM
Rwork0.1377 ---
obs0.1382 187028 88.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.28 Å2 / Biso mean: 20.908 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å2-0 Å20.06 Å2
2---0.97 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 1.55→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 296 1238 12674
Biso mean--20.11 31.63 -
Num. residues----1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01311913
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711390
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.69516181
X-RAY DIFFRACTIONr_angle_other_deg1.5041.59126590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85451521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65522.967455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6152094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3031549
X-RAY DIFFRACTIONr_chiral_restr0.1010.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022223
X-RAY DIFFRACTIONr_rigid_bond_restr3.498323299
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 121 -
Rwork0.218 11828 -
all-11949 -
obs--76.33 %

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