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- PDB-1so8: Abeta-bound human ABAD structure [also known as 3-hydroxyacyl-CoA... -

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Basic information

Entry
Database: PDB / ID: 1so8
TitleAbeta-bound human ABAD structure [also known as 3-hydroxyacyl-CoA dehydrogenase type II (Type II HADH), Endoplasmic reticulum-associated amyloid beta-peptide binding protein (ERAB)]
Components3-hydroxyacyl-CoA dehydrogenase type II
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / Rossmann fold / Abeta-induced distorsion
Function / homology
Function and homology information


brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / mitochondrial tRNA methylation / tRNA processing in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing ...brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / mitochondrial tRNA methylation / tRNA processing in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / tRNA modification in the mitochondrion / 7alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / testosterone dehydrogenase [NAD(P)] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3-hydroxyacyl-CoA dehydrogenase activity / bile acid biosynthetic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / mitochondrion organization / fatty acid metabolic process / lipid metabolic process / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLustbader, J.W. / Cirilli, M. / Wu, H.
CitationJournal: Science / Year: 2004
Title: ABAD directly links Abeta to mitochondrial toxicity in Alzheimer's disease.
Authors: Lustbader, J.W. / Cirilli, M. / Lin, C. / Xu, H.W. / Takuma, K. / Wang, N. / Caspersen, C. / Chen, X. / Pollak, S. / Chaney, M. / Trinchese, F. / Gunn-Moore, F. / Lue, L.F. / Walker, D.G. / ...Authors: Lustbader, J.W. / Cirilli, M. / Lin, C. / Xu, H.W. / Takuma, K. / Wang, N. / Caspersen, C. / Chen, X. / Pollak, S. / Chaney, M. / Trinchese, F. / Gunn-Moore, F. / Lue, L.F. / Walker, D.G. / Kuppusamy, P. / Zewier, Z.L. / Arancio, O. / Stern, D. / Yan, S.S. / Wu, H.
History
DepositionMar 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / 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_asym_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_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

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Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0284
Polymers26,9471
Non-polymers813
Water2,126118
1
A: 3-hydroxyacyl-CoA dehydrogenase type II
hetero molecules

A: 3-hydroxyacyl-CoA dehydrogenase type II
hetero molecules

A: 3-hydroxyacyl-CoA dehydrogenase type II
hetero molecules

A: 3-hydroxyacyl-CoA dehydrogenase type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,11416
Polymers107,7884
Non-polymers32612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation23_655-z+1,y,x1
2
A: 3-hydroxyacyl-CoA dehydrogenase type II
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)216,22832
Polymers215,5768
Non-polymers65124
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_656-z+1,-y,-x+11
Buried area25260 Å2
ΔGint-324 kcal/mol
Surface area63170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.000, 130.000, 130.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-301-

NA

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Components

#1: Protein 3-hydroxyacyl-CoA dehydrogenase type II / Type II HADH / Endoplasmic reticulum-associated amyloid beta-peptide binding protein (ERAB) / Short- ...Type II HADH / Endoplasmic reticulum-associated amyloid beta-peptide binding protein (ERAB) / Short-chain type dehydrogenase/reductase XH98G2


Mass: 26947.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HADH2, ERAB, XH98G2, SCHAD / Plasmid: pGE5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q99714, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.4 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Abeta, MES, NaCl, DTT, NAD, benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 17049 / % possible obs: 99.8 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 57.7
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 13 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 728424.72 / Data cutoff high rms absF: 728424.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1002 5.9 %RANDOM
Rwork0.231 ---
obs0.231 17049 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.1866 Å2 / ksol: 0.407949 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 3 118 1600
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.862.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 158 6.1 %
Rwork0.211 2427 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM

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