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- PDB-5kcp: horse liver S48T alcohol dehydrogenase complexed with NAD and pen... -

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Basic information

Entry
Database: PDB / ID: 5kcp
Titlehorse liver S48T alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Ser48 to Thr-48 substitution / Horse Liver Alcohol Dehydrogenase / NAD-pentafluorobenzyl alcohol
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. / 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
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: 1.1 Å
AuthorsPlapp, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM078446 United States
CitationJournal: Chem. Biol. Interact. / Year: 2017
Title: Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93.
Authors: Kim, K. / Plapp, B.V.
History
DepositionJun 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 12, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)82,58816
Polymers79,7352
Non-polymers2,85414
Water18,7901043
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-104 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.440, 51.590, 92.560
Angle α, β, γ (deg.)91.87, 103.06, 110.33
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: 39867.301 Da / Num. of mol.: 2 / Mutation: S48T
Source method: isolated from a genetically manipulated source
Details: horse liver alcohol dehydrogenase E isoenzyme with S48T substitution
Source: (gene. exp.) Equus caballus (horse) / Organ: Liver / Plasmid: pBPP/EqADH / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1057 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
#4: Chemical
ChemComp-PFB / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL


Mass: 198.090 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H3F5O
#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.: 1043 / 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: 2.28 Å3/Da / Density % sol: 46 % / 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 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 / Details: ADJUSTABLE FOCUS K-B PAIR SIPLUS PT, RH COATINGS
RadiationMonochromator: DOUBLE CRYSTAL CRYOCOOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.1→19.4 Å / Num. obs: 270420 / % possible obs: 89.3 % / Redundancy: 5.52 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.5
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 5.1 / % possible all: 56.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV

4dwv


Resolution: 1.1→19.4 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.701 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13805 1305 0.5 %RANDOM
Rwork0.11775 ---
obs0.11784 269109 89.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0.52 Å20.33 Å2
2--0.41 Å2-0.02 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 176 1043 6791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026028
X-RAY DIFFRACTIONr_bond_other_d0.0020.025930
X-RAY DIFFRACTIONr_angle_refined_deg1.7262.0238188
X-RAY DIFFRACTIONr_angle_other_deg0.987313789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8924.608204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.582151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4961524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216544
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021190
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.951.3643027
X-RAY DIFFRACTIONr_mcbond_other0.9491.3633026
X-RAY DIFFRACTIONr_mcangle_it1.1912.0573788
X-RAY DIFFRACTIONr_mcangle_other1.1912.0583789
X-RAY DIFFRACTIONr_scbond_it1.6081.6433001
X-RAY DIFFRACTIONr_scbond_other1.6081.6443002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8842.3724390
X-RAY DIFFRACTIONr_long_range_B_refined3.39421.8097965
X-RAY DIFFRACTIONr_long_range_B_other2.56618.7447157
X-RAY DIFFRACTIONr_rigid_bond_restr2.053311958
X-RAY DIFFRACTIONr_sphericity_free26.98510196
X-RAY DIFFRACTIONr_sphericity_bonded8.0981012713
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 62 -
Rwork0.181 11764 -
obs--52.88 %

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