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- PDB-3vzs: Crystal structure of PhaB from Ralstonia eutropha in complex with... -

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Basic information

Entry
Database: PDB / ID: 3vzs
TitleCrystal structure of PhaB from Ralstonia eutropha in complex with Acetoacetyl-CoA and NADP
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-COENZYME A / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Acetoacetyl-CoA reductase
B: Acetoacetyl-CoA reductase
C: Acetoacetyl-CoA reductase
D: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,45316
Polymers110,6894
Non-polymers6,76412
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23500 Å2
ΔGint-152 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.401, 123.445, 260.248
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

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Components

#1: Protein
Acetoacetyl-CoA reductase


Mass: 27672.285 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1M MES (pH 7.1), 1.6M ammonium sulfate, 10% 1,4-dioxane, 0.9mM NADP+, 0.9mM AcAcCoA, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 3, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 58459 / % possible obs: 96.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 17.78 Å2 / Rsym value: 0.091
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 7.86 / Rsym value: 0.303 / % possible all: 98.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1I01

1i01


Resolution: 2.14→35.121 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8817 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 18.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 2949 5.05 %
Rwork0.165 --
obs0.1672 58397 96.61 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.62 Å2 / Biso mean: 19.3094 Å2 / Biso min: 2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.14→35.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 428 627 8469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027982
X-RAY DIFFRACTIONf_angle_d0.70810862
X-RAY DIFFRACTIONf_dihedral_angle_d14.672910
X-RAY DIFFRACTIONf_chiral_restr0.0481210
X-RAY DIFFRACTIONf_plane_restr0.0021350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1381-2.17310.26391460.18092454260092
2.1731-2.21060.24531570.18162637279498
2.2106-2.25080.23641270.18382682280998
2.2508-2.29410.24421330.17682626275998
2.2941-2.34090.23141340.17382684281898
2.3409-2.39180.24361320.17692628276097
2.3918-2.44740.21931450.17412620276597
2.4474-2.50860.2111300.16592674280497
2.5086-2.57640.24051570.1672588274597
2.5764-2.65220.22261560.17372585274197
2.6522-2.73780.23481420.17542640278297
2.7378-2.83560.23351360.16912649278597
2.8356-2.9490.19921350.16562618275396
2.949-3.08320.2071370.16682610274796
3.0832-3.24560.21421370.16012605274296
3.2456-3.44880.19371460.16052599274595
3.4488-3.71480.16521300.14242618274894
3.7148-4.08820.15721250.14462595272094
4.0882-4.67860.19041300.14292659278995
4.6786-5.890.19461400.1692783292399
5.89-35.12540.21681740.187628943068100

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