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- PDB-3gk3: Crystal structure of acetoacetyl-CoA reductase from Burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 3gk3
TitleCrystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b
ComponentsAcetoacetyl-CoA reductase
KeywordsOXIDOREDUCTASE / acetoacetyl-Co reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / monocarboxylic acid metabolic process / lipid metabolic process / nucleotide binding / cytoplasm
Similarity search - Function
Acetoacetyl-CoA reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Acetoacetyl-CoA reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
PHOSPHATE ION / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)115,4998
Polymers115,1194
Non-polymers3804
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13580 Å2
ΔGint-126 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.570, 102.920, 137.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acetoacetyl-CoA reductase


Mass: 28779.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Gene: phbB-2, BURPS1710b_A1014 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JJT1, acetoacetyl-CoA reductase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6.5
Details: JCSG+ screen D12: 40mM KH2PO4, 16% PEG 8000, 20% glycerol, 0.4ul + 0.4ul, protein at 32.7mg/ml, pH 6.5, vapor diffusion, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→41.803 Å / Num. obs: 58501 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.417 Å2 / Rmerge(I) obs: 0.089
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.150.5582.414839425398
2.15-2.210.463.216980419499.7
2.21-2.280.4273.516742407199.7
2.28-2.350.354.116670398099.6
2.35-2.420.3374.216291382999.7
2.42-2.510.2854.915987373599.8
2.51-2.60.2435.615574360599.8
2.6-2.710.2076.315186349699.8
2.71-2.830.1856.714557331299.8
2.83-2.970.1438.114114320099.7
2.97-3.130.129.413419304599.5
3.13-3.320.0891312650286299.4
3.32-3.550.07117.411853270198.9
3.55-3.830.05322.110925250598.4
3.83-4.20.04426.310156229497.4
4.2-4.70.03830.19240206896
4.7-5.420.03829.68192182896
5.42-6.640.04625.16968157596.9
6.64-9.390.02835.25412123595.5
9.390.02242.7288871391.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.803 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.724 / SU ML: 0.32 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 2963 5.07 %
Rwork0.226 --
obs0.228 58440 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.418 Å2 / ksol: 0.425 e/Å3
Displacement parametersBiso max: 85.5 Å2 / Biso mean: 40.314 Å2 / Biso min: 24.18 Å2
Baniso -1Baniso -2Baniso -3
1--14.049 Å20 Å2-0 Å2
2--30.551 Å20 Å2
3----16.502 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7006 0 20 276 7302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213980
X-RAY DIFFRACTIONf_angle_d1.15625134
X-RAY DIFFRACTIONf_chiral_restr0.0921107
X-RAY DIFFRACTIONf_plane_restr0.0052240
X-RAY DIFFRACTIONf_dihedral_angle_d14.5433404
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 (%)
2.1-2.1350.3841500.3552553270397
2.135-2.1710.391360.32326182754100
2.171-2.2110.3551360.31326422778100
2.211-2.2530.4411330.30526022735100
2.253-2.2990.3671400.2982640278099
2.299-2.3490.3611350.26526692804100
2.349-2.4040.3351350.26626272762100
2.404-2.4640.3321450.25526302775100
2.464-2.5310.3221450.24326412786100
2.531-2.6050.311230.23326512774100
2.605-2.6890.3061440.22426442788100
2.689-2.7850.3111470.22526412788100
2.785-2.8970.2591400.22626542794100
2.897-3.0290.3151500.21626592809100
3.029-3.1880.281420.22626582800100
3.188-3.3880.2541490.2062648279799
3.388-3.6490.2541280.1912661278999
3.649-4.0160.2181360.1832648278498
4.016-4.5970.2071560.172610276697
4.597-5.7890.2231390.182640277996
5.789-41.8110.231540.2232741289596

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