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- PDB-6n94: Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propi... -

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Basic information

Entry
Database: PDB / ID: 6n94
TitleMethylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl-amino(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 / : / Chem-KGJ / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Methylmalonyl-CoA decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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_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)183,61924
Polymers175,1436
Non-polymers8,47618
Water33,0581835
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28560 Å2
ΔGint-153 kcal/mol
Surface area51290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.046, 114.816, 193.732
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, 1853 molecules

#2: Chemical
ChemComp-KGJ / [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]ethylamino]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium


Mass: 850.537 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H39N9O19P3
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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 / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1835 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 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: 1.75→30 Å / Num. all: 1422149 / Num. obs: 194971 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.05 / Rrim(I) all: 0.135 / Rsym value: 0.125 / Χ2: 0.907 / Net I/av σ(I): 15.346 / Net I/σ(I): 5.2 / Num. measured all: 1422149
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.489 / Mean I/σ(I) obs: 1.312 / Num. unique obs: 9703 / Rsym value: 1.489 / % 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: 6N92

6n92


Resolution: 1.75→29.29 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / Matrix type: sparse / SU B: 2.31 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 9164 5 %RANDOM
Rwork0.1457 ---
obs0.1473 175192 94.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.7 Å2 / Biso mean: 21.86 Å2 / Biso min: 5.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å2-0 Å2
2---0.15 Å20 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.75→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12246 0 550 1893 14689
Biso mean--40.1 34.19 -
Num. residues----1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01313761
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712757
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.69318875
X-RAY DIFFRACTIONr_angle_other_deg1.5091.59729706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3651752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65322.287717
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.169152354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1451590
X-RAY DIFFRACTIONr_chiral_restr0.1160.21831
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215378
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022878
X-RAY DIFFRACTIONr_mcbond_it1.851.9976453
X-RAY DIFFRACTIONr_mcbond_other1.8511.9976452
X-RAY DIFFRACTIONr_mcangle_it2.7192.9868111
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
1.748-1.7930.2733690.25169311425251.2210.235
1.793-1.8420.2534710.23399761389775.1740.214
1.842-1.8950.2586510.222119681356293.0470.2
1.895-1.9530.2316500.205123211312998.7970.181
1.953-2.0160.2346050.19121511277699.8430.164
2.016-2.0860.2216540.179117071236499.9760.156
2.086-2.1640.1976050.167112861189299.9920.145
2.164-2.2510.1915700.15510962115321000.134
2.251-2.350.1865380.14110503110411000.123
2.35-2.4630.1885070.143100581056999.9620.126
2.463-2.5940.1845170.14895671008599.990.131
2.594-2.7480.1964710.1499088956599.9370.137
2.748-2.9340.1814220.1548586901299.9560.146
2.934-3.1640.1974220.1658002842599.9880.162
3.164-3.4570.2024230.1627359778699.9490.165
3.457-3.8510.1633460.1456726708399.8450.154
3.851-4.4190.1493100.1256005633599.6840.142
4.419-5.3470.132750.1135133542099.7790.137
5.347-7.3040.172180.1534124434499.9540.19
7.304-19.9680.1821380.1542627277699.6040.199

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