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- PDB-1qlj: HORSE LIVER ALCOHOL DEHYDROGENASE APO ENZYME DOUBLE MUTANT OF GLY... -

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Basic information

Entry
Database: PDB / ID: 1qlj
TitleHORSE LIVER ALCOHOL DEHYDROGENASE APO ENZYME DOUBLE MUTANT OF GLY 293 ALA AND PRO 295 THR
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / DOUBLE MUTANT
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
Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRamaswamy, S. / Plapp, B.V.
Citation
Journal: Biochemistry / Year: 1999
Title: Substitutions in the Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer
Authors: Ramaswamy, S. / Park, D.H. / Plapp, B.V.
#1: Journal: J.Biol.Chem. / Year: 1982
Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Plapp, B.V. / Samama, J.P. / Branden, C.I.
#2: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution
Authors: Eklund, H. / Samma, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A.
History
DepositionSep 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Other / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0023
Polymers39,8711
Non-polymers1312
Water1,56787
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.140, 72.920, 180.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: generate
Matrix: (-0.999743, -0.022108, -0.00496), (-0.022112, 0.999755, 0.000652), (0.004944, 0.000761, -0.999987)
Vector: 29.3698, 0.404, 89.9955)

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Components

#1: Protein ALCOHOL DEHYDROGENASE / ADH


Mass: 39871.289 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EQUUS CABALLUS (horse) / Description: E.COLI EXPRESSED MUTANT PROTEIN / Cellular location: CYTOPLASM / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CJ236 / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTANT PROTEIN SEQUENCE NOT SUBMITTED

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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: 4.54 Å3/Da / Density % sol: 46 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 MM
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 8.4 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme11
24.5 %MPD12
350 mMtris(hydroxymethyl)aminomethane-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 15, 1997
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 17446 / % possible obs: 94.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 36.5 Å2 / Rsym value: 0.102 / Net I/σ(I): 5.9
Reflection shellResolution: 2.8→3.13 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.221 / % possible all: 87.8
Reflection
*PLUS
Num. measured all: 49060 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
% possible obs: 87.8 % / Rmerge(I) obs: 0.221

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Processing

Software
NameVersionClassification
CNS0.4refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HLD

1hld


Resolution: 2.8→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 893 4.8 %RANDOM
Rwork0.226 ---
obs0.226 18547 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--6.503 Å20 Å20 Å2
2--0.989 Å20 Å2
3---5.514 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 2 87 2874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.1

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