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- PDB-5vml: Crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 5vml
TitleCrystal Structure of Acetoacetyl-CoA Reductase from Burkholderia Pseudomallei 1710b with bound NADP
ComponentsAcetoacetyl-CoA reductase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / : / short chain dehydrogenase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia Pseudomallei 1710b with bound NADP
Authors: Dranow, D.M. / Conrady, D.G. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9183
Polymers29,0571
Non-polymers8622
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,67412
Polymers116,2274
Non-polymers3,4468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area18390 Å2
ΔGint-133 kcal/mol
Surface area34240 Å2
MethodPISA
3
A: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8376
Polymers58,1142
Non-polymers1,7234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5550 Å2
ΔGint-43 kcal/mol
Surface area20760 Å2
MethodPISA
4
A: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8376
Polymers58,1142
Non-polymers1,7234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6110 Å2
ΔGint-40 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.310, 66.310, 115.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

21A-662-

HOH

31A-675-

HOH

DetailsMonomer as determined by gel filtration.

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Components

#1: Protein Acetoacetyl-CoA reductase


Mass: 29056.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: phbB-1, BURPS1710b_2329 / Plasmid: BupsA.00010.e.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JRS9, acetoacetyl-CoA reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: BupsA.00010.e.A1.PS00061 at 19.3 mg/ml incubated with 4 mM NADP, mixed 1:1 with Morpheus(c8): 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MOPS/ HEPES-Na, pH = 7.5, 0. ...Details: BupsA.00010.e.A1.PS00061 at 19.3 mg/ml incubated with 4 mM NADP, mixed 1:1 with Morpheus(c8): 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MOPS/ HEPES-Na, pH = 7.5, 0.03 M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate, crystals were soaked for 24 hours with 5 mM NADP in well solution, harvested directly

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 2, 2017
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 28909 / % possible obs: 99.5 % / Redundancy: 8.9 % / Biso Wilson estimate: 15.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.03
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.458 / Num. unique obs: 1965 / CC1/2: 0.856 / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX(dev_2744)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EZL

3ezl


Resolution: 1.7→46.888 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.81
RfactorNum. reflection% reflection
Rfree0.1709 2030 7.02 %
Rwork0.1443 --
obs0.1461 28908 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.31 Å2 / Biso mean: 19.0649 Å2 / Biso min: 7.89 Å2
Refinement stepCycle: final / Resolution: 1.7→46.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 56 289 2187
Biso mean--20.6 31.52 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052006
X-RAY DIFFRACTIONf_angle_d0.7722735
X-RAY DIFFRACTIONf_chiral_restr0.054304
X-RAY DIFFRACTIONf_plane_restr0.004371
X-RAY DIFFRACTIONf_dihedral_angle_d15.1621210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.26421350.22471759189493
1.7425-1.78960.22491490.197918732022100
1.7896-1.84230.22641380.178819092047100
1.8423-1.90170.19461460.164718762022100
1.9017-1.96970.1861430.160518652008100
1.9697-2.04860.18991430.150419212064100
2.0486-2.14180.1861380.148219272065100
2.1418-2.25470.16841300.134519182048100
2.2547-2.3960.15721650.136418962061100
2.396-2.5810.15811540.145819112065100
2.581-2.84070.18821490.150819482097100
2.8407-3.25160.17751420.140619552097100
3.2516-4.09640.12751340.118420012135100
4.0964-46.90610.15931640.135721192283100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.50540.4433-0.14840.97590.03161.81950.0309-0.15970.06280.07080.0307-0.0349-0.06460.2362-0.04220.1118-0.00680.00020.1379-0.03570.08621.830315.013320.5202
20.55870.3250.02251.17370.18440.49170.0169-0.0961-0.01210.05180.0204-0.05620.0074-0.0118-0.03970.08350.00930.00270.11950.00190.0976.2916.773419.1785
31.6904-0.70790.0171.75280.65441.0693-0.0197-0.08-0.10160.1420.1274-0.10490.15120.1141-0.0690.1260.006-0.01680.11530.00660.089116.18163.4365.437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 66 )A4 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 176 )A67 - 176
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 248 )A177 - 248

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