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- PDB-1e3s: Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH -

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Basic information

Entry
Database: PDB / ID: 1e3s
TitleRat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH
ComponentsSHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / BETA-OXIDATION OF FATTY ACIDS / STEROIDS / AMYLOID BINDING
Function / homology
Function and homology information


Mitochondrial protein degradation / acetoacetyl-CoA reductase activity / Branched-chain amino acid catabolism / 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 / mitochondrial tRNA methylation / mitochondrial ribonuclease P complex ...Mitochondrial protein degradation / acetoacetyl-CoA reductase activity / Branched-chain amino acid catabolism / 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 / mitochondrial tRNA methylation / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / 7alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase (NAD+) activity / C21-steroid hormone metabolic process / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / L-isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / testosterone dehydrogenase (NAD+) activity / bile acid biosynthetic process / 17beta-estradiol 17-dehydrogenase / Leydig cell differentiation / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / steroid binding / fatty acid metabolic process / nuclear estrogen receptor binding / mitochondrion organization / male gonad development / NAD binding / amyloid-beta binding / protein homotetramerization / tRNA binding / endoplasmic reticulum / mitochondrion / identical protein binding
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPowell, A.J. / Read, J.A. / Banfield, M.J. / Brady, R.L.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Recognition of Structurally Diverse Substrates by Type II 3-Hydroxyacyl-Coa Dehydrogenase (Hadh II) Amyloid-Beta Binding Alcohol Dehydrogenase (Abad)
Authors: Powell, A.J. / Read, J.A. / Banfield, M.J. / Gunn-Moore, F. / Yan, S.D. / Lustbader, J. / Stern, A.R. / Stern, D.M. / Brady, R.L.
History
DepositionJun 22, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE
B: SHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE
C: SHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE
D: SHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7448
Polymers109,0904
Non-polymers2,6544
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.280, 68.960, 69.550
Angle α, β, γ (deg.)64.84, 72.51, 74.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE / HADH II


Mass: 27272.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cellular location: CYTOPLASM / Organ: BRAIN / Organelle: MITOCHONRIA / Plasmid: PET15B / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: O70351, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP PROT: 5MG/ML, 0.75 MM NADH, 50 MM NACL, 10 MM HEPES PH 7.5 WELL: 30% PEG 4000, 0.2 M LI SO4, 0.1 M TRIS PH 8.5. 18 C
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %(w/v)PEG40001reservoir
20.2 M1reservoirLiSO4
30.1 MTris1reservoir
45 mg/mlprotein1drop
5750 MNADH1drop
650 mM1dropNaCl
710 mMHEPES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 62009 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 13
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.227 / % possible all: 91.6

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HSD

2hsd


Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3014 5 %RANDOM
Rwork0.189 ---
obs-62009 94.9 %-
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 0 176 492 7605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 55813 / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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