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- PDB-3vzp: Crystal structure of PhaB from Ralstonia eutropha -

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Basic information

Entry
Database: PDB / ID: 3vzp
TitleCrystal structure of PhaB 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 / 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
1,4-DIETHYLENE DIOXIDE / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 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: 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)112,16320
Polymers110,6894
Non-polymers1,47316
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16440 Å2
ΔGint-168 kcal/mol
Surface area35260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.700, 123.690, 260.790
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: 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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 100490 / % possible obs: 97.7 % / Redundancy: 7.18 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.108
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 7 % / Num. unique all: 14615 / Rsym value: 0.666 / % possible all: 89.2

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I01

1i01


Resolution: 1.792→20.059 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8296 / SU ML: 0.25 / σ(F): 1.99 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 4993 4.97 %RANDOM
Rwork0.1915 ---
obs0.1938 100465 97.8 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.538 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso max: 83.91 Å2 / Biso mean: 21.2802 Å2 / Biso min: 7.86 Å2
Baniso -1Baniso -2Baniso -3
1-12.3971 Å2-0 Å2-0 Å2
2---7.357 Å20 Å2
3----5.04 Å2
Refinement stepCycle: LAST / Resolution: 1.792→20.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 89 692 8195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077614
X-RAY DIFFRACTIONf_angle_d0.97810281
X-RAY DIFFRACTIONf_dihedral_angle_d12.1752695
X-RAY DIFFRACTIONf_chiral_restr0.071159
X-RAY DIFFRACTIONf_plane_restr0.0051322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7925-1.81280.3967720.34661718179053
1.8128-1.83420.35061650.28533183334899
1.8342-1.85650.32241550.2633203335899
1.8565-1.880.31121730.24983157333099
1.88-1.90470.30721730.23983207338099
1.9047-1.93080.30381560.23393185334199
1.9308-1.95840.28591630.22583220338399
1.9584-1.98760.25091490.22033183333299
1.9876-2.01860.28021650.21813233339899
2.0186-2.05160.24231680.20463171333999
2.0516-2.0870.26051620.2043206336899
2.087-2.12490.25171670.19913213338099
2.1249-2.16570.25211730.19253193336699
2.1657-2.20990.26011970.19063204340199
2.2099-2.25790.22761550.18523215337099
2.2579-2.31030.25251530.18593201335499
2.3103-2.3680.22881760.18623241341799
2.368-2.43190.24011740.191232583432100
2.4319-2.50340.25371640.19423203336799
2.5034-2.5840.23631890.18313220340999
2.584-2.67610.24431880.187731753363100
2.6761-2.7830.22741850.182532523437100
2.783-2.90930.24171500.185432803430100
2.9093-3.06220.22421800.192832733453100
3.0622-3.25330.23441700.183632273397100
3.2533-3.50330.22121810.182332823463100
3.5033-3.85360.19341610.164432773438100
3.8536-4.4060.20041640.160533463510100
4.406-5.53180.19541680.165433153483100
5.5318-20.05990.23831970.2043431362899

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