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- PDB-1e3w: Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NAD... -

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Basic information

Entry
Database: PDB / ID: 1e3w
TitleRat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH and 3-keto butyrate
Components(SHORT CHAIN 3-HYDROXYACYL-COA ...) x 2
KeywordsDEHYDROGENASE / BETA-OXIDATION OF FATTY ACIDS / STEROIDS / AMYLOID BINDING
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 / mitochondrial tRNA methylation / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-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 / 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 / cholate 7-alpha-dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / C21-steroid hormone metabolic process / acetoacetyl-CoA reductase activity / Branched-chain amino acid catabolism / 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 / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase 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 / mitochondrion organization / fatty acid metabolic process / nuclear estrogen receptor binding / 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
ACETOACETIC ACID / 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. / 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 26, 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 1.3Jul 12, 2017Group: Derived calculations / Category: struct_conn
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_data_processing_status / struct_conn / struct_conn_type
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 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)112,66417
Polymers109,0624
Non-polymers3,60313
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.603, 67.426, 67.500
Angle α, β, γ (deg.)65.22, 73.27, 75.67
Int Tables number1
Space group name H-MP1

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Components

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SHORT CHAIN 3-HYDROXYACYL-COA ... , 2 types, 4 molecules ABCD

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


Mass: 27244.434 Da / Num. of mol.: 1
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: Protein SHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE / 3-HYDROXYACYL-COA DEHYDROGENASE TYPE II (HADH II)


Mass: 27272.510 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 902 molecules

#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-AAE / ACETOACETIC ACID / Acetoacetic acid


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 10MG/ML, 0.4 MM ACETOACETYL COA, 1 MM NADH, 10 MM HEP WELL: 28% 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 148442 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 19.7
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.291 / % possible all: 60.4
Reflection
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 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. atoms7342 0 232 889 8463
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: 141062 / Num. reflection Rfree: 7380 / Rfactor obs: 0.157 / Rfactor Rfree: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.028

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