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- PDB-3rmu: Crystal structure of human Methylmalonyl-CoA epimerase, MCEE -

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Basic information

Entry
Database: PDB / ID: 3rmu
TitleCrystal structure of human Methylmalonyl-CoA epimerase, MCEE
ComponentsMethylmalonyl-CoA epimerase, mitochondrial
KeywordsISOMERASE / structural genomics consortium / SGC / vitamin B12 / mitochondria
Function / homology
Function and homology information


methylmalonyl-CoA epimerase / short-chain fatty acid catabolic process / methylmalonyl-CoA epimerase activity / L-methylmalonyl-CoA metabolic process / Propionyl-CoA catabolism / mitochondrial matrix / mitochondrion / metal ion binding
Similarity search - Function
Methylmalonyl-CoA epimerase / : / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / Methylmalonyl-CoA epimerase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChaikuad, A. / Krysztofinska, E. / Froese, D.S. / Yue, W.W. / Vollmar, M. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Chaikuad, A. / Krysztofinska, E. / Froese, D.S. / Yue, W.W. / Vollmar, M. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human Methylmalonyl-CoA epimerase, MCEE
Authors: Chaikuad, A. / Krysztofinska, E. / Froese, D.S. / Yue, W.W. / Vollmar, M. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, U. / ...Authors: Chaikuad, A. / Krysztofinska, E. / Froese, D.S. / Yue, W.W. / Vollmar, M. / Muniz, J.R.C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionApr 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylmalonyl-CoA epimerase, mitochondrial
B: Methylmalonyl-CoA epimerase, mitochondrial
C: Methylmalonyl-CoA epimerase, mitochondrial
D: Methylmalonyl-CoA epimerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,38532
Polymers57,5284
Non-polymers1,85828
Water5,819323
1
A: Methylmalonyl-CoA epimerase, mitochondrial
B: Methylmalonyl-CoA epimerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,68917
Polymers28,7642
Non-polymers92515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-44 kcal/mol
Surface area13350 Å2
MethodPISA
2
C: Methylmalonyl-CoA epimerase, mitochondrial
D: Methylmalonyl-CoA epimerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,69715
Polymers28,7642
Non-polymers93313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-31 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.120, 66.690, 76.980
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methylmalonyl-CoA epimerase, mitochondrial / MCEE / DL-methylmalonyl-CoA racemase


Mass: 14381.883 Da / Num. of mol.: 4 / Fragment: UNP residues 45-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCEE / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q96PE7, methylmalonyl-CoA epimerase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsR104L IS A NATURAL VARIANT

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG smears (PEG400, PEG550 MME, PEG600, PEG1000), 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2010 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→38.49 Å / Num. all: 49557 / Num. obs: 49519 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2 / Num. unique all: 7219 / % possible all: 99.7

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 30A4

30a4


Resolution: 1.8→36.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.435 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.135 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23722 2491 5 %RANDOM
Rwork0.18701 ---
obs0.18961 47027 99.14 %-
all-49519 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.591 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20.11 Å2
2--2.72 Å20 Å2
3----0.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.235 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 109 323 4415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224219
X-RAY DIFFRACTIONr_bond_other_d0.0010.022877
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9945649
X-RAY DIFFRACTIONr_angle_other_deg0.91537140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0835552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.15726.107149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54815744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.022155
X-RAY DIFFRACTIONr_chiral_restr0.0930.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
X-RAY DIFFRACTIONr_mcbond_it2.88332690
X-RAY DIFFRACTIONr_mcbond_other0.93231098
X-RAY DIFFRACTIONr_mcangle_it4.26854320
X-RAY DIFFRACTIONr_scbond_it7.2481529
X-RAY DIFFRACTIONr_scangle_it9.977111319
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 185 -
Rwork0.331 3452 -
obs--99.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.68220.5538-0.11161.7477-0.71333.72460.0104-0.5367-0.18610.0653-0.01390.0354-0.04330.02960.00350.02010.0020.00660.08150.03040.013731.592826.567872.2455
24.3306-0.82822.84410.9135-1.08085.62630.2154-0.037-0.551-0.1083-0.03950.16420.5901-0.3185-0.17580.118-0.0330.03390.0527-0.0020.134521.634620.475163.8725
315.9098-4.975-1.62018.51934.299614.5522-0.0325-0.0737-1.02290.1195-0.17710.57150.6719-0.94090.20960.0984-0.0382-0.00080.12910.06090.133817.326923.749561.961
43.2741-0.4847-0.00311.98620.83313.8405-0.0110.4148-0.3017-0.1059-0.01220.01280.01540.15410.02330.0311-0.00250.01340.0589-0.03790.032833.293426.231749.8596
54.54921.0492.61761.27461.47824.67840.1437-0.0976-0.69690.07230.0179-0.19040.47590.2618-0.16160.11430.04160.04290.03680.04520.149542.984820.195158.0882
610.90715.097-2.07737.3428-1.359411.88940.0407-0.1459-0.92220.0154-0.1412-0.51930.57820.82120.10050.08250.0507-0.01270.1345-0.03730.150747.208923.121360.5393
73.73240.1135-0.53970.6023-0.54813.7729-0.05760.36970.5038-0.0243-0.0272-0.0084-0.25440.08720.08480.0635-0.0125-0.02110.04280.05470.082743.334453.136545.1804
86.734-1.7242-6.11982.3454.900820.14160.16450.15340.8644-0.33590.0468-0.0148-1.0896-0.6285-0.21120.14330.0357-0.02050.13450.00130.22228.192553.408956.0869
916.1288.1058-2.569121.3067-0.39654.07720.718-1.24981.32821.1479-0.6599-0.3278-0.2981-0.5118-0.05820.0929-0.00440.01550.2422-0.12910.197535.53153.693157.273
103.93211.12631.22061.50180.71073.70860.0001-0.55750.2651-0.015-0.0306-0.0610.0135-0.11660.03060.02370.00160.00090.0933-0.05250.033847.817550.578165.4755
113.3434-0.9275-1.25211.85121.82986.45770.12340.10510.5631-0.1911-0.0989-0.1064-0.62430.302-0.02440.1075-0.0324-0.03190.04390.03640.143257.8956.139757.0709
1214.1822-3.79870.64995.9086-2.292310.57080.00930.05341.13320.1018-0.2323-0.4702-0.59621.1810.22310.1003-0.05620.01060.165-0.01880.166461.882153.011954.9771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 94
2X-RAY DIFFRACTION2A95 - 144
3X-RAY DIFFRACTION3A145 - 176
4X-RAY DIFFRACTION4B-1 - 94
5X-RAY DIFFRACTION5B95 - 143
6X-RAY DIFFRACTION6B144 - 176
7X-RAY DIFFRACTION7C-1 - 134
8X-RAY DIFFRACTION8C135 - 163
9X-RAY DIFFRACTION9C164 - 176
10X-RAY DIFFRACTION10D-1 - 94
11X-RAY DIFFRACTION11D95 - 144
12X-RAY DIFFRACTION12D145 - 176

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