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- PDB-4n5l: Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 4n5l
TitleCrystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from Ralstonia eutropha
ComponentsAcetoacetyl-CoA reductase
KeywordsOXIDOREDUCTASE / alpha/beta structure
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / monocarboxylic acid metabolic process / lipid metabolic process / cytoplasm
Similarity search - Function
Acetoacetyl-CoA reductase / : / short chain dehydrogenase / PKS_KR / 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 ...Acetoacetyl-CoA reductase / : / short chain dehydrogenase / PKS_KR / 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
Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsKim, J.-E. / Kim, S. / Kim, K.-J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha
Authors: Kim, J.-E. / Chang, J.H. / Kim, E.-J. / Kim, K.-J.
History
DepositionOct 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetoacetyl-CoA reductase
B: Acetoacetyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)58,7982
Polymers58,7982
Non-polymers00
Water5,603311
1
A: Acetoacetyl-CoA reductase
B: Acetoacetyl-CoA reductase

A: Acetoacetyl-CoA reductase
B: Acetoacetyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)117,5974
Polymers117,5974
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13010 Å2
ΔGint-90 kcal/mol
Surface area35100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.912, 94.341, 137.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acetoacetyl-CoA reductase / (R)-3-hydroxybutyrylCoA dehydrogenase


Mass: 29399.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: H16 / Gene: phbB / Plasmid: pProEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P14697, acetoacetyl-CoA reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ethanol,citrate, lithium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→68.64 Å / Num. all: 68610 / Num. obs: 59854 / % possible obs: 87.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.059 / Rsym value: 0.051 / Net I/σ(I): 30
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.65-1.68181.9
1.68-1.71187.7
1.71-1.74188.1
1.74-1.78187.7
1.78-1.82187.5
1.82-1.86186.6
1.86-1.9186.3
1.9-1.96187.1
1.96-2.01187.6
2.01-2.08187.4
2.08-2.15187.5
2.15-2.24185.9
2.24-2.34185.5
2.34-2.46185.5
2.46-2.62186.1
2.62-2.82186.7
2.82-3.11187.8
3.11-3.55188.8
3.55-4.48189.9
4.48-50192.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q7B

1q7b


Resolution: 1.65→32.18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.942 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2916 3034 5.1 %RANDOM
Rwork0.2453 ---
all0.2477 59851 --
obs0.2477 56817 87.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.54 Å2 / Biso mean: 23.1289 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å2-0 Å2
2--1.71 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 0 311 3983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193730
X-RAY DIFFRACTIONr_bond_other_d0.0010.023590
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9385044
X-RAY DIFFRACTIONr_angle_other_deg0.90838228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30624.43158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66715632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3141524
X-RAY DIFFRACTIONr_chiral_restr0.1180.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02856
X-RAY DIFFRACTIONr_mcbond_it1.8932.1731950
X-RAY DIFFRACTIONr_mcbond_other1.8872.1731949
X-RAY DIFFRACTIONr_mcangle_it2.583.2542434
LS refinement shellResolution: 1.651→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 229 -
Rwork0.39 3923 -
all-4152 -
obs--82.51 %

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