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- PDB-4ks9: Crystal Structure of Malonyl-CoA decarboxylase (Rmet_2797) from C... -

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Basic information

Entry
Database: PDB / ID: 4ks9
TitleCrystal Structure of Malonyl-CoA decarboxylase (Rmet_2797) from Cupriavidus metallidurans, Northeast Structural Genomics Consortium Target CrR76
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
Similarity search - Function
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 ...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 speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsForouhar, F. / Tran, T.H. / Lew, S. / Seetharaman, J. / Xiao, R. / Acton, T.B. / Everett, J.K. / 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,1113
Polymers96,0872
Non-polymers241
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-17 kcal/mol
Surface area36180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.015, 69.392, 74.362
Angle α, β, γ (deg.)90.000, 103.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Malonyl-CoA decarboxylase /


Mass: 48043.578 Da / Num. of mol.: 2 / Fragment: UNP residues 57-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: matA, Rmet_2797, Rmet_2797 (MCD) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q1LJK6, malonyl-CoA decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.5
Details: Protein solution: 20 mM Tris (pH 7), 250 mM NaCl, 5% (v/v) glycerol, 3 mM malonyl-CoA. Precipitation solution: 160 mM magnesium chloride, 80 mM Tris (pH 8.5), 24% (w/v) PEG4000, 20% (v/v) ...Details: Protein solution: 20 mM Tris (pH 7), 250 mM NaCl, 5% (v/v) glycerol, 3 mM malonyl-CoA. Precipitation solution: 160 mM magnesium chloride, 80 mM Tris (pH 8.5), 24% (w/v) PEG4000, 20% (v/v) glycerol, and 3% (v/v) ethanol, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 24, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 43263 / Num. obs: 44261 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.055 / Net I/σ(I): 23
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4419 / Rsym value: 0.386 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNS1.3refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of MCD from Rhodopseudomonas palustris, which will be deposited after this entry.

Resolution: 2.3→28.75 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 392997 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 3765 10 %RANDOM
Rwork0.239 ---
all0.241 42214 --
obs0.24 37613 89.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.817 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 101.81 Å2 / Biso mean: 46.196 Å2 / Biso min: 16.95 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å20 Å20.53 Å2
2--3.65 Å20 Å2
3----7.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 0 1 276 6535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 478 9.5 %
Rwork0.286 4555 -
all-5033 -
obs-3765 72.2 %

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