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- PDB-4n5m: Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 4n5m
TitleCrystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from Ralstonia eutropha in complexed with acetoacetyl-CoA
ComponentsAcetoacetyl-CoA reductase
KeywordsOXIDOREDUCTASE / alpha/beta structure
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic 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-COENZYME A / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.34 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 ...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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Acetoacetyl-CoA reductase
B: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,05410
Polymers58,7982
Non-polymers2,2568
Water9,782543
1
A: Acetoacetyl-CoA reductase
B: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
B: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,10820
Polymers117,5974
Non-polymers4,51216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area20620 Å2
ΔGint-70 kcal/mol
Surface area34250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.570, 139.570, 70.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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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: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
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: 0.97949 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 24, 2013
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 151127 / % possible obs: 99.4 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 56.5
Reflection shellResolution: 1.34→1.37 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.6 / % possible all: 99

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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: 1.34→23.39 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.825 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 7752 5 %RANDOM
Rwork0.1681 ---
obs0.1691 146641 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.61 Å2 / Biso mean: 19.4431 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-0 Å2
2--0.57 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.34→23.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 144 543 4389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193911
X-RAY DIFFRACTIONr_bond_other_d0.0010.023728
X-RAY DIFFRACTIONr_angle_refined_deg2.4461.9785294
X-RAY DIFFRACTIONr_angle_other_deg1.04838551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7485492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15724.465159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72315641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6421524
X-RAY DIFFRACTIONr_chiral_restr0.1750.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02882
X-RAY DIFFRACTIONr_mcbond_it2.0131.4571971
X-RAY DIFFRACTIONr_mcbond_other2.0041.4571970
X-RAY DIFFRACTIONr_mcangle_it2.9732.1792462
LS refinement shellResolution: 1.34→1.375 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 551 -
Rwork0.303 10598 -
all-11149 -
obs--98.14 %

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