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- PDB-4ksa: Crystal Structure of Malonyl-CoA decarboxylase from Rhodopseudomo... -

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Basic information

Entry
Database: PDB / ID: 4ksa
TitleCrystal Structure of Malonyl-CoA decarboxylase from Rhodopseudomonas palustris, Northeast Structural Genomics Consortium Target RpR127
ComponentsMalonyl-CoA decarboxylase
KeywordsLYASE / NESGC / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / alpha-beta two-domained protein
Function / homology
Function and homology information


malonyl-CoA decarboxylase / malonyl-CoA decarboxylase activity / fatty acid biosynthetic process / identical protein binding
Similarity search - Function
Aminopeptidase - #180 / Malonyl-CoA decarboxylase, oligemerization domain / Malonyl-CoA decarboxylase, catalytic domain / Malonyl-CoA decarboxylase, C-terminal / Malonyl-CoA decarboxylase, N-terminal / Malonyl-CoA decarboxylase, N-terminal domain superfamily / Malonyl-CoA decarboxylase / Malonyl-CoA decarboxylase, C-terminal catalytic domain superfamily / Malonyl-CoA decarboxylase C-terminal domain / Malonyl-CoA decarboxylase N-terminal domain ...Aminopeptidase - #180 / Malonyl-CoA decarboxylase, oligemerization domain / Malonyl-CoA decarboxylase, catalytic domain / Malonyl-CoA decarboxylase, C-terminal / Malonyl-CoA decarboxylase, N-terminal / Malonyl-CoA decarboxylase, N-terminal domain superfamily / Malonyl-CoA decarboxylase / Malonyl-CoA decarboxylase, C-terminal catalytic domain superfamily / Malonyl-CoA decarboxylase C-terminal domain / Malonyl-CoA decarboxylase N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Aminopeptidase / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Malonyl-CoA decarboxylase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Structure / Year: 2013
Title: Crystal structures of malonyl-coenzyme a decarboxylase provide insights into its catalytic mechanism and disease-causing mutations.
Authors: Froese, D.S. / Forouhar, F. / Tran, T.H. / Vollmar, M. / Kim, Y.S. / Lew, S. / Neely, H. / Seetharaman, J. / Shen, Y. / Xiao, R. / Acton, T.B. / Everett, J.K. / Cannone, G. / Puranik, S. / ...Authors: Froese, D.S. / Forouhar, F. / Tran, T.H. / Vollmar, M. / Kim, Y.S. / Lew, S. / Neely, H. / Seetharaman, J. / Shen, Y. / Xiao, R. / Acton, T.B. / Everett, J.K. / Cannone, G. / Puranik, S. / Savitsky, P. / Krojer, T. / Pilka, E.S. / Kiyani, W. / Lee, W.H. / Marsden, B.D. / von Delft, F. / Allerston, C.K. / Spagnolo, L. / Gileadi, O. / Montelione, G.T. / Oppermann, U. / Yue, W.W. / Tong, L.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malonyl-CoA decarboxylase
B: Malonyl-CoA decarboxylase
C: Malonyl-CoA decarboxylase
D: Malonyl-CoA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,6136
Polymers201,5644
Non-polymers492
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-36 kcal/mol
Surface area73670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.505, 159.765, 108.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Malonyl-CoA decarboxylase /


Mass: 50390.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: MLYCD (RPA0560), MLYCD/MCD, RPA0560 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6NCB2, malonyl-CoA decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 291 K / pH: 8.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Precipitation solution: 0.1M magnesium nitrate, 100 mM Tris (pH 8.5), and 33% (v/v) PEG 400, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 4, 2010 / 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→30 Å / Num. all: 131748 / Num. obs: 130826 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.042 / Net I/σ(I): 25.37
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.46 / Num. unique all: 13216 / Rsym value: 0.493 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
CNS1.3refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.89 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 610248 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 12191 9.9 %RANDOM
Rwork0.225 ---
obs0.226 123627 94.7 %-
all-130545 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.592 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 159.08 Å2 / Biso mean: 69.01 Å2 / Biso min: 21.23 Å2
Baniso -1Baniso -2Baniso -3
1-4.26 Å20 Å20 Å2
2--6.78 Å20 Å2
3----11.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13233 0 2 207 13442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 1858 10.1 %
Rwork0.34 16602 -
all-18460 -
obs-16602 85 %

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