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- PDB-6n93: Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propi... -

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Basic information

Entry
Database: PDB / ID: 6n93
TitleMethylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl-oxa(dethia)-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
IMIDAZOLE / : / (2E)-2-(hydroxyimino)propanoic acid / Chem-KGA / NICKEL (II) ION / Methylmalonyl-CoA decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: 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 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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)183,52724
Polymers175,1436
Non-polymers8,38318
Water35,3991965
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28000 Å2
ΔGint-147 kcal/mol
Surface area51610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.179, 114.653, 194.554
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 , 7 types, 1983 molecules

#2: Chemical
ChemComp-KGA / [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]ethoxy]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium / 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]ethyl 2-nitropropanoate


Mass: 851.521 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H38N8O20P3
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / 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-KG7 / (2E)-2-(hydroxyimino)propanoic acid


Mass: 103.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1965 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 150 mM sodium chloride, 100 mM imidazole, 0.4 M Monosodium phosphate/1.6 M Dipotassium phosphate, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 203268 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Rsym value: 0.11 / Χ2: 0.888 / Net I/av σ(I): 14.375 / Net I/σ(I): 5.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.192 / Mean I/σ(I) obs: 1.167 / Num. unique obs: 10028 / Rsym value: 1.192 / % possible all: 93.8

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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: 6N92

6n92


Resolution: 1.7→28.68 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Matrix type: sparse / SU B: 2.178 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1004 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.098
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1839 9300 5 %RANDOM
Rwork0.153 ---
obs0.1546 177818 86.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 148.25 Å2 / Biso mean: 16.898 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2---0.3 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.7→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12246 0 472 2018 14736
Biso mean--41.97 29.1 -
Num. residues----1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01313719
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712763
X-RAY DIFFRACTIONr_angle_refined_deg1.811.68418819
X-RAY DIFFRACTIONr_angle_other_deg1.4781.59329716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32651765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03522.224715
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.792152357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0021590
X-RAY DIFFRACTIONr_chiral_restr0.0950.21835
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215362
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022883
X-RAY DIFFRACTIONr_mcbond_it1.5941.4856466
X-RAY DIFFRACTIONr_mcbond_other1.5951.4856465
X-RAY DIFFRACTIONr_mcangle_it2.5182.2198130
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
1.692-1.7360.2853220.2758051579538.7910.26
1.736-1.7830.2724440.25589941539761.2980.239
1.783-1.8340.2655790.235112731492079.4370.215
1.834-1.890.2476150.225123221459888.6220.2
1.89-1.9520.2486660.216122081412191.1690.188
1.952-2.0190.226130.184120151366092.4450.159
2.019-2.0950.2035650.171116401321392.3710.149
2.095-2.1790.1976050.158111861274792.50.138
2.179-2.2750.2055840.172106021220491.6580.152
2.275-2.3850.1755180.139102441171191.8970.122
2.385-2.5120.1885150.14497711116592.1270.13
2.512-2.6610.1834550.1493131060492.1160.13
2.661-2.8410.24730.1498875994394.0160.142
2.841-3.0640.1974640.1588532932996.430.154
3.064-3.3480.2134260.1688061862098.4570.171
3.348-3.7310.1713680.1547268782297.6220.162
3.731-4.2830.163230.1326600699498.9850.147
4.283-5.1860.1483150.1215663599699.70.143
5.186-7.0990.2092450.1654532477999.9580.203
7.099-19.9780.161440.1622880304599.310.217

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