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- PDB-6cxx: Horse liver E267H alcohol dehydrogenase complex with 3'-dephospho... -

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Basic information

Entry
Database: PDB / ID: 6cxx
TitleHorse liver E267H alcohol dehydrogenase complex with 3'-dephosphocoenzyme A
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / NAD-dependent horse liver alcohol dehydrogenase E267H mutant 3'-dephosphocoenzyme A
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
DEPHOSPHO COENZYME A / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsPlapp, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AA00279 United States
CitationJournal: Arch. Biochem. Biophys. / Year: 2018
Title: Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A.
Authors: Kim, Y.H. / Gogerty, D.S. / Plapp, B.V.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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)82,07014
Polymers79,7252
Non-polymers2,34612
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-134 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.210, 73.080, 181.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 39862.305 Da / Num. of mol.: 2 / Mutation: E267H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: liver / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 562 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H35N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 8.4
Details: 10 mg/ml protein dialyzed against 50 mM tris(hydroxymethyl)aminomethane-HCl, 0.25 mM EDTA, with methylpentanediol increasing to 25 %.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.26→20 Å / Num. obs: 191863 / % possible obs: 96.6 % / Redundancy: 6.24 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.042 / Rrim(I) all: 0.105 / Χ2: 1.21 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.26-1.316.580.6352.1196150.490.2690.6911.3999.9
1.31-1.366.650.5732.5195880.6231.499.9
1.36-1.426.640.5112.9196600.5551.3699.8
1.42-1.496.60.4313.4196550.4691.3299.8
1.49-1.596.520.3414.2197030.3711.3199.9
1.59-1.716.390.2545.4197270.2771.2299.8
1.71-1.886.150.1637.6197240.1791.0799.5
1.88-2.155.660.09711.4190660.1070.9395.8
2.15-2.715.460.06616173060.0730.8686.4
2.71-19.825.560.04528.1178190.051.0286.4

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8Ldata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QLH

1qlh


Resolution: 1.26→20 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.658 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.049
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1951 1 %RANDOM
Rwork0.1724 ---
obs0.1727 189852 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.57 Å2 / Biso mean: 18.185 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--1.4 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: final / Resolution: 1.26→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 140 553 6265
Biso mean--23.33 27.6 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195923
X-RAY DIFFRACTIONr_bond_other_d0.0020.025788
X-RAY DIFFRACTIONr_angle_refined_deg1.9722.0018031
X-RAY DIFFRACTIONr_angle_other_deg1.056313488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4415760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0924.343198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.298151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6131524
X-RAY DIFFRACTIONr_chiral_restr0.1130.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021097
X-RAY DIFFRACTIONr_rigid_bond_restr2.865311711
X-RAY DIFFRACTIONr_sphericity_free17.90110349
X-RAY DIFFRACTIONr_sphericity_bonded5.9291011808
LS refinement shellResolution: 1.26→1.293 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 128 -
Rwork0.391 14280 -
all-14408 -
obs--99.83 %

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