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- PDB-5cds: I220L horse liver alcohol dehydrogenase complexed with NAD and pe... -

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Basic information

Entry
Database: PDB / ID: 5cds
TitleI220L horse liver alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol / Rossmann fold
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. / 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: 1.4 Å
AuthorsPlapp, B.V. / Shanmuganatham, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 078446 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis.
Authors: Shanmuganatham, K.K. / Wallace, R.S. / Lee, A.T. / Plapp, B.V.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 3, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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

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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)81,92812
Polymers79,7072
Non-polymers2,22110
Water15,565864
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-19 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.270, 51.530, 92.440
Angle α, β, γ (deg.)91.75, 103.12, 109.34
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 / Mutation: I220L
Source method: isolated from a genetically manipulated source
Details: I220F substitution of wild-type horse liver alcohol dehydrogenase E1
Source: (gene. exp.) Equus caballus (horse) / Organ: Liver / Plasmid: pBPP/EqADH1E / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 874 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) / Nicotinamide adenine dinucleotide


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.: 2 / Source method: obtained synthetically / Formula: C7H3F5O
#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.: 864 / 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: columns
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-,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.8 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 132451 / % possible obs: 91 % / Redundancy: 3.64 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.3
Reflection shellResolution: 1.4→1.436 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.3 / % possible all: 86.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
d*TREKdata reduction
d*TREKdata scaling
Omodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV

4dwv


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.816 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18411 1340 1 %RANDOM
Rwork0.13194 ---
obs0.13246 132451 91.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.63 Å2-0.14 Å2
2--1.57 Å2-0.08 Å2
3----2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 134 864 6568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.025934
X-RAY DIFFRACTIONr_bond_other_d0.0010.025847
X-RAY DIFFRACTIONr_angle_refined_deg1.7022.0178046
X-RAY DIFFRACTIONr_angle_other_deg0.877313578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86724.581203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.072151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4741524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021176
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_it2.1272.0072994
X-RAY DIFFRACTIONr_mcbond_other2.1272.0062993
X-RAY DIFFRACTIONr_mcangle_it2.3563.0233740
X-RAY DIFFRACTIONr_mcangle_other2.3563.0233741
X-RAY DIFFRACTIONr_scbond_it3.5752.3542940
X-RAY DIFFRACTIONr_scbond_other3.5812.3552941
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8993.3934305
X-RAY DIFFRACTIONr_long_range_B_refined4.37818.7337488
X-RAY DIFFRACTIONr_long_range_B_other3.78917.3676901
X-RAY DIFFRACTIONr_rigid_bond_restr3.726311781
X-RAY DIFFRACTIONr_sphericity_free30.41210203
X-RAY DIFFRACTIONr_sphericity_bonded10.3021012361
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 99 -
Rwork0.271 9313 -
obs--86.77 %

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