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- PDB-4ksf: Crystal Structure of Malonyl-CoA decarboxylase from Agrobacterium... -

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Basic information

Entry
Database: PDB / ID: 4ksf
TitleCrystal Structure of Malonyl-CoA decarboxylase from Agrobacterium vitis, Northeast Structural Genomics Consortium Target RiR35
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 activity / fatty acid biosynthetic process / identical protein binding
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
NICKEL (II) ION / Malonyl-CoA decarboxylase
Similarity search - Component
Biological speciesAgrobacterium vitis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, 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 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malonyl-CoA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8814
Polymers51,7521
Non-polymers1303
Water41423
1
A: Malonyl-CoA decarboxylase
hetero molecules

A: Malonyl-CoA decarboxylase
hetero molecules

A: Malonyl-CoA decarboxylase
hetero molecules

A: Malonyl-CoA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,52516
Polymers207,0064
Non-polymers51812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area10830 Å2
ΔGint-136 kcal/mol
Surface area73020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.412, 100.412, 242.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-501-

NI

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Components

#1: Protein Malonyl-CoA decarboxylase /


Mass: 51751.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium vitis (bacteria) / Strain: S4 / Gene: Avi_5372, MCD (Avi_5372) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: B9K0V9
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Precipitation solution: 200 mM ammonium sulfate and 20% (w/v) PEG3350, 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: Jul 11, 2011 / 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: 3.1→30 Å / Num. all: 21471 / Num. obs: 21321 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 48.4 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.078 / Net I/σ(I): 15.94
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.65 / Num. unique all: 2158 / Rsym value: 0.497 / % possible all: 99.8

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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: 4KSA

4ksa


Resolution: 3.1→28.14 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 199793 / 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
Rfree0.291 1801 9.5 %RANDOM
Rwork0.22 ---
all0.226 21503 --
obs0.223 19052 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.569 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 112.53 Å2 / Biso mean: 58.477 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å20 Å2
2--2.67 Å20 Å2
3----5.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.1→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 3 23 3257
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 253 10 %
Rwork0.261 2279 -
all-2532 -
obs-2279 70.5 %

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