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- PDB-4ng5: V203A horse liver alcohol dehydrogenase E complexed with NAD+ and... -

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Basic information

Entry
Database: PDB / ID: 4ng5
TitleV203A horse liver alcohol dehydrogenase E complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Rossmann fold / dehydrogenase / NAD / liver cytosol
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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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.
CitationJournal: Biochemistry / Year: 2014
Title: Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis.
Authors: Yahashiri, A. / Rubach, J.K. / Plapp, B.V.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 12, 2020Group: Database references / Category: pdbx_related_exp_data_set / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)82,10814
Polymers79,6502
Non-polymers2,45712
Water18,9521052
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-104 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.520, 51.560, 92.550
Angle α, β, γ (deg.)91.80, 103.05, 110.30
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: 39825.223 Da / Num. of mol.: 2 / Mutation: V203A
Source method: isolated from a genetically manipulated source
Details: tac promoter / Source: (gene. exp.) Equus caballus (horse) / Strain: domestic horse / Plasmid: pBPP/EqADH E / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1064 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.: 2 / 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.: 1052 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 50 mM ammonium N-[tris(hydrozymethyl)methyl]-2-aminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 13-25 % 2- ...Details: 50 mM ammonium N-[tris(hydrozymethyl)methyl]-2-aminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 13-25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007
Details: ADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS DOUBLE CRYSTAL CRYOCOOLED SI(111)
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→20 Å / Num. all: 261399 / % possible obs: 86.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.25 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.5
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 3.8 / Num. unique all: 16455 / % possible all: 54.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.7.0032refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DWV

4dwv


Resolution: 1.1→17.91 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.702 / SU ML: 0.015 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13655 2681 1 %RANDOM
Rwork0.11968 ---
all0.11985 261399 --
obs0.11985 258723 86.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.529 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0.63 Å20.28 Å2
2--0.42 Å20.04 Å2
3----0.59 Å2
Refine analyzeLuzzati coordinate error free: 0.026 Å
Refinement stepCycle: LAST / Resolution: 1.1→17.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 150 1052 6768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026099
X-RAY DIFFRACTIONr_bond_other_d0.0010.026031
X-RAY DIFFRACTIONr_angle_refined_deg1.7922.028287
X-RAY DIFFRACTIONr_angle_other_deg0.885314039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12924.651215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.093151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9571526
X-RAY DIFFRACTIONr_chiral_restr0.1050.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021204
X-RAY DIFFRACTIONr_mcbond_it1.0671.4113041
X-RAY DIFFRACTIONr_mcbond_other1.0661.413040
X-RAY DIFFRACTIONr_mcangle_it1.2892.1293808
X-RAY DIFFRACTIONr_mcangle_other1.2892.1293809
X-RAY DIFFRACTIONr_scbond_it2.0331.7093058
X-RAY DIFFRACTIONr_scbond_other2.0351.713059
X-RAY DIFFRACTIONr_scangle_other2.3432.4564471
X-RAY DIFFRACTIONr_long_range_B_refined3.71314.4667990
X-RAY DIFFRACTIONr_long_range_B_other2.79612.6687168
X-RAY DIFFRACTIONr_rigid_bond_restr3.337312130
X-RAY DIFFRACTIONr_sphericity_free36.62210214
X-RAY DIFFRACTIONr_sphericity_bonded9.1641012875
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 116 -
Rwork0.317 11177 -
obs--50.36 %

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