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- PDB-1ydo: Crystal Structure of the Bacillis subtilis HMG-CoA Lyase, Northea... -

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Basic information

Entry
Database: PDB / ID: 1ydo
TitleCrystal Structure of the Bacillis subtilis HMG-CoA Lyase, Northeast Structural Genomics Target SR181.
ComponentsHMG-CoA Lyase
KeywordsLYASE / TIM-barrel protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA lyase / hydroxymethylglutaryl-CoA lyase activity / ketone body biosynthetic process / L-leucine catabolic process / lipid metabolic process / metal ion binding
Similarity search - Function
HMG-CoA lyase / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Hydroxymethylglutaryl-CoA lyase YngG
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.71 Å
AuthorsForouhar, F. / Hussain, M. / Edstrom, W. / Vorobiev, S.M. / Xiao, R. / Ciano, M. / Shih, L. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Forouhar, F. / Hussain, M. / Edstrom, W. / Vorobiev, S.M. / Xiao, R. / Ciano, M. / Shih, L. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bonds.
Authors: Forouhar, F. / Hussain, M. / Farid, R. / Benach, J. / Abashidze, M. / Edstrom, W.C. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Fu, Z. / Kim, J.J. / Miziorko, H.M. / Montelione, G.T. / Hunt, J.F.
History
DepositionDec 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HMG-CoA Lyase
B: HMG-CoA Lyase
C: HMG-CoA Lyase
D: HMG-CoA Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8228
Polymers136,3154
Non-polymers5084
Water7,278404
1
A: HMG-CoA Lyase
B: HMG-CoA Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4114
Polymers68,1572
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-11 kcal/mol
Surface area22200 Å2
MethodPISA
2
C: HMG-CoA Lyase
D: HMG-CoA Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4114
Polymers68,1572
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-11 kcal/mol
Surface area22310 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-41 kcal/mol
Surface area42420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.693, 104.666, 97.445
Angle α, β, γ (deg.)90.00, 107.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HMG-CoA Lyase / hypothetical protein BSU18230


Mass: 34078.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Species: Bacillus subtilis / Strain: 168 / Gene: yngG / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O34873
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.4 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 100 mM NaI, and 10 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→28.94 Å / Num. all: 64017 / Num. obs: 61067 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.068 / Net I/σ(I): 15.11
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.66 / Rsym value: 0.297 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.71→28.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 297512.17 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 5147 9.8 %RANDOM
Rwork0.263 ---
obs0.263 52284 81.7 %-
all-61067 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.104 Å2 / ksol: 0.292026 e/Å3
Displacement parametersBiso mean: 48.3 Å2
Baniso -1Baniso -2Baniso -3
1-15.47 Å20 Å223.59 Å2
2---22.43 Å20 Å2
3---6.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.71→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9152 0 4 404 9560
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 608 9.7 %
Rwork0.332 5629 -
obs--57.6 %

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