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- PDB-2oxi: REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE... -

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Entry
Database: PDB / ID: 2oxi
TitleREFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE(NAD(A)-CHOH(D))
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
COPPER (II) ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsAl-Karadaghi, S. / Cedergren-Zeppezauer, E.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 A resolution.
Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Dauter, Z. / Wilson, K.S.
#1: Journal: FEBS Lett. / Year: 1992
Title: Copper(II)-Substituted Horse Liver Alcohol Dehydrogenase: Structure of the Minor Species
Authors: Formicka, G. / Zeppezauer, M. / Fey, F. / Huettermann, J.
#2: Journal: Biochim.Biophys.Acta / Year: 1987
Title: Electronic Absorption and Epr Spectroscopy of Copper Alcohol Dehydrogenase: Pink, Violet and Green Forms of a Type 1 Copper Center Analog
Authors: Maret, W. / Kozlowski, H.
#3: Journal: J.Am.Chem.Soc. / Year: 1986
Title: Resonance Raman Spectroscopy of Blue Copper Proteins: Ligand and Coenzyme Effects in Copper(II)-Substituted Liver Alcohol Dehydrogenase
Authors: Maret, W. / Shiemke, A.K. / Wheeler, W.D. / Loehr, T.M. / Sanders-Loehr, J.
#4: Journal: Biochemistry / Year: 1983
Title: Resonance Raman Spectra of Copper(II)-Substituted Liver Alcohol Dehydrogenase: A Type 1 Copper Analogue
Authors: Maret, W. / Zeppezauer, M. / Sanders-Loehr, J. / Loehr, T.M.
#5: Journal: Biochim.Biophys.Acta / Year: 1983
Title: An Epr Study of the Blue Copper Center in Horse Liver Alcohol Dehydrogenase
Authors: Maret, W. / Zeppezauer, M. / Desideri, A. / Morpurgo, L. / Rotilio, G.
#6: Journal: FEBS Lett. / Year: 1981
Title: Ligand Binding to the Blue Copper Center of Horse Liver Alcohol Dehydrogenase
Authors: Maret, W. / Zeppezauer, M. / Desideri, A. / Morpurgo, L. / Rotilio, G.
#7: Journal: J.Inorg.Biochem. / Year: 1980
Title: Active Site-Specific Reconstituted Copper(II) Horse Liver Alcohol Dehydrogenase: A Biological Model for Type 1 Cu and its Changes Upon Ligand Binding and Conformational Transitions
Authors: Maret, W. / Dietrich, H. / Ruf, H.-H. / Zeppezauer, M.
History
DepositionNov 8, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
Remark 650HELIX RESIDUES GLY 181 - VAL 189 OF HELICES *HAA* AND *HAB* FORM A PI-HELIX (CLASS 3, 1.5 TURNS).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,44810
Polymers79,7072
Non-polymers1,7418
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-63 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.400, 180.600, 50.800
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 62 / 2: CIS PROLINE - PRO B 62
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.49169, 0.12942, -0.86109), (0.12449, -0.98918, -0.07758), (-0.86182, -0.06906, -0.50249)
Vector: 25.1531, 0.2546, 43.3583)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. CORRESP. EULERIAN ANGLES (THETA1, THETA2, THETA3) 274.5813 120.1650 264.8520 CORRESP. SPHERICAL POLAR ANGLES (PSI, PHI, KAPPA) 85.7848 30.0067 180.2826 CORRESP. ROTATION ANGLE 179.7174 ABOUT AXIS -0.8636 -0.0735 0.4987

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALCOHOL DEHYDROGENASE


Mass: 39853.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 453 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.75 mMNADH11
21.5 %(v/v)DMSO11
30.05 MTris-HCl11pH8.2
410 %MPD11

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 12 Å / Num. obs: 41119 / Num. measured all: 81533 / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.16 / Rfactor obs: 0.16 / Highest resolution: 2.1 Å
Details: THERE IS DISCRETE DISORDER IN RESIDUES CYS A 46 CYS A 281 CYS A 282 CYS B 46 CYS B 282
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 100 445 6125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 12 Å / Num. reflection obs: 41119 / Rfactor obs: 0.161 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2

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