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- PDB-6n95: Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propi... -

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Basic information

Entry
Database: PDB / ID: 6n95
TitleMethylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-CoA
ComponentsMethylmalonyl-CoA decarboxylase
KeywordsLYASE / crotonase / beta-keto / isostere
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
: / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / (2R)-sulfonatepropionyl-CoA / (2S)-sulfonatepropionyl-CoA / Methylmalonyl-CoA decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsStunkard, L.M. / Dixon, A.D. / Huth, T.J. / Lohman, J.R.
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies.
Authors: Stunkard, L.M. / Dixon, A.D. / Huth, T.J. / Lohman, J.R.
History
DepositionNov 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
B: Methylmalonyl-CoA decarboxylase
C: Methylmalonyl-CoA decarboxylase
D: Methylmalonyl-CoA decarboxylase
E: Methylmalonyl-CoA decarboxylase
F: Methylmalonyl-CoA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,73926
Polymers175,1436
Non-polymers11,59620
Water30,5171694
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28190 Å2
ΔGint-156 kcal/mol
Surface area50230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.927, 114.421, 193.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Methylmalonyl-CoA decarboxylase / MMCD / Transcarboxylase


Mass: 29190.557 Da / Num. of mol.: 6 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: scpB, mmcD, ygfG, b2919, JW2886 / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P52045, Lyases; Carbon-carbon lyases; Carboxy-lyases

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Non-polymers , 8 types, 1714 molecules

#2: Chemical
ChemComp-YXS / (2S)-sulfonatepropionyl-CoA / (2~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propane-2-sulfonic acid


Mass: 903.661 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40N7O20P3S2
#3: Chemical
ChemComp-YXR / (2R)-sulfonatepropionyl-CoA / (2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]me thoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfany l]-1-oxidanylidene-propane-2-sulfonic acid


Mass: 903.661 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40N7O20P3S2
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1694 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200 mM sodium chloride, 100 mM imidazole, 0.4 Monosodium phosphate/1.6 M Dipotassium phosphate, 4% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 8, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.798→30 Å / Num. obs: 178862 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.065 / Rrim(I) all: 0.177 / Rsym value: 0.165 / Χ2: 1.05 / Net I/av σ(I): 12.972 / Net I/σ(I): 4.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.395 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 17657 / Rsym value: 1.395 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0230phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EF8

1ef8


Resolution: 1.798→19.997 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / Matrix type: sparse / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.102
RfactorNum. reflection% reflection
Rfree0.1922 8931 4.999 %
Rwork0.1593 --
obs-178638 99.688 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.421 Å2
Baniso -1Baniso -2Baniso -3
1--0.009 Å2-0 Å20 Å2
2--0.008 Å20 Å2
3---0.002 Å2
Refinement stepCycle: final / Resolution: 1.798→19.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12246 0 713 1777 14736
Biso mean--40.32 37.29 -
Num. residues----1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01413278
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712030
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.69518111
X-RAY DIFFRACTIONr_angle_other_deg1.0421.65528232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2351646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23222.191680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.005152276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8251586
X-RAY DIFFRACTIONr_chiral_restr0.1380.21760
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022408
X-RAY DIFFRACTIONr_nbd_refined0.2230.22735
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.211667
X-RAY DIFFRACTIONr_nbtor_refined0.1770.26450
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.25810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.21046
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0240.23
X-RAY DIFFRACTIONr_metal_ion_refined0.330.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.219
X-RAY DIFFRACTIONr_nbd_other0.2660.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0020.21
X-RAY DIFFRACTIONr_mcbond_it1.9932.3096331
X-RAY DIFFRACTIONr_mcbond_other1.9932.3096330
X-RAY DIFFRACTIONr_mcangle_it2.7733.4527928
X-RAY DIFFRACTIONr_mcangle_other2.7733.4527929
X-RAY DIFFRACTIONr_scbond_it3.3812.8066947
X-RAY DIFFRACTIONr_scbond_other3.3812.8066947
X-RAY DIFFRACTIONr_scangle_it5.0974.06910136
X-RAY DIFFRACTIONr_scangle_other5.0964.06910137
X-RAY DIFFRACTIONr_lrange_it6.26429.29115179
X-RAY DIFFRACTIONr_lrange_other6.25629.24815140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.798-1.8440.2966410.272120541306897.1460.254
1.844-1.8940.2766320.254120531269099.9610.233
1.894-1.9490.2536300.23211693123231000.206
1.949-2.0080.2485860.209114231201099.9920.181
2.008-2.0730.2186320.189110341166799.9910.167
2.073-2.1450.225430.179107321127699.9910.158
2.145-2.2250.2135210.16310386109071000.146
2.225-2.3150.1985200.1499987105071000.134
2.315-2.4160.1935320.1469590101221000.132
2.416-2.5330.1994660.159173964099.990.136
2.533-2.6670.2034170.154881892351000.143
2.667-2.8260.1954330.1558300873499.9890.145
2.826-3.0170.1924290.158781682451000.153
3.017-3.2520.2073980.1677309770999.9740.165
3.252-3.5530.193430.1586758710299.9860.162
3.553-3.9570.1683430.146169651399.9850.15
3.957-4.540.1542810.118548757681000.13
4.54-5.490.1252280.117475149791000.134
5.49-7.4860.1882110.147376039711000.164
7.486-19.9970.1341450.1482414256099.9610.178

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