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- PDB-3vzr: Crystal structure of T173S mutant of PhaB from Ralstonia eutropha -

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Basic information

Entry
Database: PDB / ID: 3vzr
TitleCrystal structure of T173S mutant of PhaB from Ralstonia eutropha
ComponentsAcetoacetyl-CoA reductase
KeywordsOXIDOREDUCTASE / alpha/beta fold
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 speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsIkeda, K. / Tanaka, Y. / Tanaka, I. / Yao, M.
CitationJournal: Appl.Environ.Microbiol. / Year: 2013
Title: Directed evolution and structural analysis of NADPH-dependent Acetoacetyl Coenzyme A (Acetoacetyl-CoA) reductase from Ralstonia eutropha reveals two mutations responsible for enhanced kinetics
Authors: Matsumoto, K. / Tanaka, Y. / Watanabe, T. / Motohashi, R. / Ikeda, K. / Tobitani, K. / Yao, M. / Tanaka, I. / Taguchi, S.
History
DepositionOct 15, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references / Structure summary
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
B: Acetoacetyl-CoA reductase
A: Acetoacetyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)55,3172
Polymers55,3172
Non-polymers00
Water00
1
B: Acetoacetyl-CoA reductase
A: Acetoacetyl-CoA reductase

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


Theoretical massNumber of molelcules
Total (without water)110,6334
Polymers110,6334
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area12880 Å2
ΔGint-88 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.671, 185.892, 75.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acetoacetyl-CoA reductase


Mass: 27658.260 Da / Num. of mol.: 2 / Mutation: T173S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: phbB, H16_A1439 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14697, acetoacetyl-CoA reductase

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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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.6-1.2M sodium / potassium tartrate, 0.16-0.2M lithium sulfate, 0.1M CHES (pH 8.9-9.9). , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 18, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 11342 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rsym value: 0.179
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.15 / Num. unique all: 1108 / Rsym value: 0.514 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VZP

3vzp


Resolution: 2.901→19.996 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8569 / SU ML: 0.24 / σ(F): 0 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 543 4.8 %random
Rwork0.1886 ---
obs0.1911 11314 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.16 Å2 / Biso mean: 24.3067 Å2 / Biso min: 6.22 Å2
Refinement stepCycle: LAST / Resolution: 2.901→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 0 0 3668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053726
X-RAY DIFFRACTIONf_angle_d0.8375036
X-RAY DIFFRACTIONf_dihedral_angle_d13.9161336
X-RAY DIFFRACTIONf_chiral_restr0.06572
X-RAY DIFFRACTIONf_plane_restr0.003654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9007-3.19150.28531220.2338263899
3.1915-3.65090.24751370.19992659100
3.6509-4.59060.23591410.1723266699
4.5906-19.99650.211430.16812808100

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