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- PDB-3vzq: Crystal structure of Q47L mutant of PhaB from Ralstonia eutropha -

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Basic information

Entry
Database: PDB / ID: 3vzq
TitleCrystal structure of Q47L 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,3152
Polymers55,3152
Non-polymers00
Water7,332407
1
A: Acetoacetyl-CoA reductase
B: Acetoacetyl-CoA reductase

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


Theoretical massNumber of molelcules
Total (without water)110,6294
Polymers110,6294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12870 Å2
ΔGint-90 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.570, 88.630, 70.680
Angle α, β, γ (deg.)90.00, 104.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-378-

HOH

31B-434-

HOH

41B-471-

HOH

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Components

#1: Protein Acetoacetyl-CoA reductase


Mass: 27657.314 Da / Num. of mol.: 2 / Mutation: Q47L
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 37627 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.183
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.07 / Num. unique all: 5945 / Rsym value: 0.498 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VZP

3vzp


Resolution: 2→45.347 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8133 / SU ML: 0.24 / σ(F): 1.99 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 1879 5 %random
Rwork0.2353 ---
obs0.2369 37575 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.91 Å2 / Biso mean: 13.9521 Å2 / Biso min: 4.65 Å2
Refinement stepCycle: LAST / Resolution: 2→45.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 0 407 4075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023726
X-RAY DIFFRACTIONf_angle_d0.6115038
X-RAY DIFFRACTIONf_dihedral_angle_d10.7981334
X-RAY DIFFRACTIONf_chiral_restr0.042576
X-RAY DIFFRACTIONf_plane_restr0.002652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0003-2.05440.28381390.24872631277095
2.0544-2.11490.27371450.244727572902100
2.1149-2.18310.2461440.243127362880100
2.1831-2.26120.27131450.23827502895100
2.2612-2.35170.28231450.22627542899100
2.3517-2.45870.26241450.23927542899100
2.4587-2.58830.29831450.239527562901100
2.5883-2.75050.27081440.246327372881100
2.7505-2.96280.27951460.2427732919100
2.9628-3.26090.27721440.240927342878100
3.2609-3.73250.24941450.21722772291799
3.7325-4.70180.23411470.211227762923100
4.7018-45.35910.28591450.25722766291198

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