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- PDB-1ef9: THE CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1ef9
TitleTHE CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE COMPLEXED WITH 2S-CARBOXYPROPYL COA
ComponentsMETHYLMALONYL COA DECARBOXYLASE
KeywordsLYASE / methylmalonyl coa decarboxylase / 2S-carboxypropyl
Function / homology
Function and homology information


methyl/ethyl malonyl-CoA decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / fatty acid beta-oxidation / cytosol
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-CARBOXYPROPYL-COENZYME A / Methylmalonyl-CoA decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsBenning, M.M. / Haller, T. / Gerlt, J.A. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2000
Title: New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli.
Authors: Benning, M.M. / Haller, T. / Gerlt, J.A. / Holden, H.M.
History
DepositionFeb 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHYLMALONYL COA DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0602
Polymers29,2071
Non-polymers8541
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.7, 142.4, 89.7
Angle α, β, γ (deg.)90.0, 109.2, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein METHYLMALONYL COA DECARBOXYLASE


Mass: 29206.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P52045, EC: 4.1.1.41
#2: Chemical ChemComp-2CP / 2-CARBOXYPROPYL-COENZYME A


Mass: 853.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O18P3S

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, 50 mM magnesium chloride, 100 mM MES, 5 mM sodium azide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %PEG80001reservoir
250 mM1reservoirMgCl2
3100 mMMES1reservoir
45 mMsodium azide1reservoir
52.5 mMinhibitor1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 49630 / Num. obs: 49630 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.44 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.3
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.152 / Num. unique all: 5502 / % possible all: 75
Reflection
*PLUS
% possible obs: 87 % / Rmerge(I) obs: 0.043

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
FRAMBOdata collection
XDSdata scaling
RefinementResolution: 2.7→30 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: STANDARD TNT GEOMETRY LIBRARY
RfactorNum. reflection% reflection
all0.19 49630 -
obs0.19 -87 %
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 54 0 2104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.27
X-RAY DIFFRACTIONt_trig_c_planes0.007
X-RAY DIFFRACTIONt_gen_planes0.009
X-RAY DIFFRACTIONt_dihedral_angle_d20.2
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / σ(F): 0 / Rfactor all: 0.19 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.27
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.2
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.009

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