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- PDB-6qh4: Crystal structure of human Methylmalonyl-CoA epimerase (MCEE) p.A... -

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Basic information

Entry
Database: PDB / ID: 6qh4
TitleCrystal structure of human Methylmalonyl-CoA epimerase (MCEE) p.Arg143Cys variant
ComponentsMethylmalonyl-CoA epimerase, mitochondrial
KeywordsISOMERASE / Methylmalonyl-CoA epimerase / mitochondrial
Function / homology
Function and homology information


methylmalonyl-CoA epimerase / methylmalonyl-CoA epimerase activity / L-methylmalonyl-CoA metabolic process / short-chain fatty acid catabolic 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: 1.922 Å
AuthorsBailey, H.J. / Chaikuid, A. / Krysztofinska, E. / Froese, D.S. / Sorrell, F.J. / Diaz-Saez, L. / Kennedy, E. / Edwards, A.M. / Bountra, C. / Yue, W.W.
CitationJournal: To Be Published
Title: Crystal structure of human Methylmalonyl-CoA epimerase (MCEE) p.Arg143Cys variant
Authors: Bailey, H.J. / Chaikuid, A. / Krysztofinska, E. / Froese, D.S. / Sorrell, F.J. / Diaz-Saez, L. / Kennedy, E. / Edwards, A.M. / Bountra, C. / Yue, W.W.
History
DepositionJan 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,4348
Polymers67,1984
Non-polymers2364
Water1,62190
1
C: Methylmalonyl-CoA epimerase, mitochondrial
A: Methylmalonyl-CoA epimerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7174
Polymers33,5992
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-58 kcal/mol
Surface area12420 Å2
MethodPISA
2
B: Methylmalonyl-CoA epimerase, mitochondrial
hetero molecules

D: Methylmalonyl-CoA epimerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7174
Polymers33,5992
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area3390 Å2
ΔGint-58 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.162, 66.990, 77.125
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 or resid 45 through 58...
21(chain B and (resid 3 or resid 45 through 46...
31(chain C and (resid 3 or resid 45 through 65...
41(chain D and (resid 3 or resid 45 through 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 or resid 45 through 58...A3
121(chain A and (resid 3 or resid 45 through 58...A45 - 58
131(chain A and (resid 3 or resid 45 through 58...A59
141(chain A and (resid 3 or resid 45 through 58...A43 - 176
151(chain A and (resid 3 or resid 45 through 58...A43 - 176
161(chain A and (resid 3 or resid 45 through 58...A43 - 176
171(chain A and (resid 3 or resid 45 through 58...A43 - 176
211(chain B and (resid 3 or resid 45 through 46...B3
221(chain B and (resid 3 or resid 45 through 46...B45 - 46
231(chain B and (resid 3 or resid 45 through 46...B47
241(chain B and (resid 3 or resid 45 through 46...B44 - 176
251(chain B and (resid 3 or resid 45 through 46...B44 - 176
261(chain B and (resid 3 or resid 45 through 46...B44 - 176
271(chain B and (resid 3 or resid 45 through 46...B44 - 176
281(chain B and (resid 3 or resid 45 through 46...B44 - 176
311(chain C and (resid 3 or resid 45 through 65...C3
321(chain C and (resid 3 or resid 45 through 65...C45 - 65
331(chain C and (resid 3 or resid 45 through 65...C66
341(chain C and (resid 3 or resid 45 through 65...C37 - 176
351(chain C and (resid 3 or resid 45 through 65...C37 - 176
361(chain C and (resid 3 or resid 45 through 65...C37 - 176
371(chain C and (resid 3 or resid 45 through 65...C37 - 176
381(chain C and (resid 3 or resid 45 through 65...C37 - 176
411(chain D and (resid 3 or resid 45 through 46...D3
421(chain D and (resid 3 or resid 45 through 46...D45 - 46
431(chain D and (resid 3 or resid 45 through 46...D47
441(chain D and (resid 3 or resid 45 through 46...D43 - 176
451(chain D and (resid 3 or resid 45 through 46...D43 - 176
461(chain D and (resid 3 or resid 45 through 46...D43 - 176
471(chain D and (resid 3 or resid 45 through 46...D43 - 176
481(chain D and (resid 3 or resid 45 through 46...D43 - 176
491(chain D and (resid 3 or resid 45 through 46...D43 - 176

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Components

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


Mass: 16799.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCEE / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q96PE7, methylmalonyl-CoA epimerase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG4000, 10% 2-propanol and 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→77.13 Å / Num. obs: 19630 / % possible obs: 48.5 % / Redundancy: 3.3 % / CC1/2: 0.997 / Net I/σ(I): 7.2
Reflection shellResolution: 1.92→2.12 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 983 / CC1/2: 0.56 / % possible all: 10.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RMU

3rmu


Resolution: 1.922→77.125 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.85
RfactorNum. reflection% reflection
Rfree0.2756 1028 5.24 %
Rwork0.2278 --
obs0.2302 19625 47.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.34 Å2 / Biso mean: 35.6023 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: final / Resolution: 1.922→77.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 4 90 3940
Biso mean--41.63 30.03 -
Num. residues----534
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1468X-RAY DIFFRACTION0.87TORSIONAL
12B1468X-RAY DIFFRACTION0.87TORSIONAL
13C1468X-RAY DIFFRACTION0.87TORSIONAL
14D1468X-RAY DIFFRACTION0.87TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9217-2.02310.4485100.33881721823
2.0231-2.14980.3934620.33321103116520
2.1498-2.31580.275970.30511758185531
2.3158-2.54890.34921270.29422245237240
2.5489-2.91770.30431610.28233048320954
2.9177-3.6760.30782600.22574641490183
3.676-77.18710.23573110.19615630594198
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)
17.15273.80641.10485.11161.67884.13260.32860.13540.63830.33550.02560.22490.05480.46560.18210.3384-0.05910.0480.4759-0.27770.28263.623728.538334.2551
22.981-1.71060.81831.4287-1.32961.8805-0.0010.3615-0.3361-0.07880.03080.40380.0097-0.0778-0.14640.10770.02250.02720.1723-0.03180.2777-8.849112.479710.9279
36.2265-1.5613-2.1563.11490.07120.99870.24910.03540.6843-0.155-0.1085-0.0961-0.05090.3952-0.15020.13760.01610.00680.4069-0.04030.1423-3.572415.94757.0987
43.2394-0.69660.01134.2297-0.36334.13160.31711.3998-0.21530.0196-0.6033-0.26360.3836-0.28730.15170.1269-0.0430.01090.3609-0.06930.2843-1.60411.851411.6096
55.20460.8461-0.59423.88170.19862.574-0.0091-0.3269-0.2293-0.3489-0.0280.17220.06530.30320.07820.1076-0.00410.01060.3111-0.00280.16470.38389.831518.8617
63.91642.45890.89126.79020.14518.2487-0.06560.3982-0.4827-0.4190.1948-0.48830.45080.4926-0.10080.09510.1088-0.02120.496-0.00660.31313.300115.421924.1013
73.7554-3.0077-3.85766.86613.93814.1253-0.2278-0.3458-0.21350.050.70280.10690.44830.8694-0.15160.2826-0.1409-0.03110.45920.06420.39113.9996.842229.3279
85.58852.32223.0314.37114.13325.8122-0.40171.55750.7851-1.05450.21860.4274-0.44520.3640.28870.23810.0244-0.10730.71880.05180.17936.976517.790621.3161
93.643-0.4487-0.0371.5798-0.42841.31820.0823-0.23920.15870.0206-0.0174-0.1372-0.29720.22850.25550.20840.06050.05970.0699-0.01680.1432-10.991115.867925.5875
105.56570.0587-0.41782.2660.68691.96290.0531-0.68240.3231-0.00190.1692-0.09-0.10640.2977-0.04870.227-0.00920.01750.29020.01670.16960.950216.15737.9086
110.9118-0.48191.20926.0087-1.68581.79340.1213-0.33030.01710.04620.13150.6382-0.12140.01650.51960.26420.00220.05820.1026-0.12960.1045-13.028114.333837.7663
123.46464.3425-3.30339.4698-5.93544.0168-0.30780.00460.1880.36680.526-0.3182-0.1621-0.6207-0.29810.1209-0.0020.03780.2667-0.00020.1225-6.934116.224431.3328
131.8418-1.10830.71551.67-1.16582.2282-0.00610.0616-0.06880.1821-0.18850.10820.137-0.41460.070.1422-0.091-0.00490.3741-0.07110.2395-16.73669.738325.414
140.10930.43410.46791.73021.71484.231-0.1061-0.1757-0.82-0.01790.1902-0.4342-0.07030.2948-0.20190.1742-0.00210.02440.7271-0.02060.4189-24.219413.515324.1221
156.8752-1.91430.86751.623-1.71732.10830.49711.1135-1.6089-0.3845-0.38390.23461.12210.2310.27320.53020.111-0.04110.3074-0.08030.43-17.63248.017418.8233
162.731-2.16751.8832.045-0.47994.5380.0779-0.71940.08010.3891-0.3573-0.0434-0.252-0.25390.0160.144-0.2207-0.01990.38960.02420.2056-18.826316.816723.5316
173.18611.10182.15758.43881.5693.2222-0.405-0.0123-0.34010.55830.07110.45710.7874-0.17380.15060.13-0.07710.04710.11880.03240.179-28.52266.5497-11.9716
186.2093-1.64762.01491.0594-1.82583.7752-0.0413-0.0010.4814-0.2092-0.3566-0.12020.0481-0.4081-1.077-0.0305-0.05520.20890.3879-0.1720.1785-40.18989.3092-0.9395
195.93552.38071.11353.03910.03680.95470.2366-0.4013-0.79620.0579-0.1139-0.41820.0327-0.13020.02920.1812-0.00770.01730.5208-0.03990.2625-38.593.4427-1.1043
203.51883.13880.61112.89830.02582.74460.246-0.1628-0.47270.20480.1862-0.72330.32580.618-0.45340.0749-0.0331-0.07860.2778-0.17840.2352-25.29467.7518-0.8554
212.3643.21092.15835.39683.44682.7756-0.0850.3187-0.05390.14020.1055-0.09670.0859-0.39340.6149-0.0012-0.1498-0.17580.3853-0.26150.0088-31.47646.2287-7.2711
226.279-0.80014.34572.52850.02916.5514-0.8538-0.0011.17230.24570.147-0.8403-1.3341.30840.53770.326-0.0458-0.11850.6334-0.19020.5218-21.582418.7942-1.6263
234.1303-2.8816-1.8314.3131-1.68155.1055-0.49490.54950.68230.25830.35130.3579-0.81380.14320.15880.302-0.0507-0.00770.1782-0.13290.4639-30.311920.8823-9.3431
245.9190.5713-3.83083.2673-0.97756.388-0.433-0.3662-0.7839-0.2828-0.504-0.14890.20340.7630.3190.2071-0.0242-0.0070.24140.09540.2393-15.33283.6549-20.2837
250.3917-0.47511.68720.6324-2.00967.3699-0.07650.56040.58850.3044-0.6625-0.4165-0.97012.01460.65990.492-0.1874-0.06190.8070.06110.4047-12.412110.8997-19.1835
264.7993-0.4644-1.7264.43920.03626.2970.4961-0.80080.55290.5438-0.2709-0.2808-0.35320.4814-0.38630.2812-0.0192-0.0270.392-0.06650.154-17.08725.7287-11.321
270.6722-0.36830.50220.9126-1.15281.45620.16960.42740.4191-0.2283-0.3002-0.5848-0.3620.08770.66840.61910.2960.02290.3650.17340.6063-22.515815.5614-23.0244
284.6369-2.3988-0.33958.20762.07252.5933-0.3146-0.7-0.76630.53890.02251.06340.32040.066-0.25690.17120.09840.07690.18330.0680.232-19.61114.5186-15.33
291.0368-0.52980.75154.17522.11283.70990.17470.0194-0.1372-0.2746-0.167-0.2208-0.04390.3022-0.12950.20560.0282-0.0470.32920.0260.2879-15.633939.473619.407
302.85490.7727-0.33344.2397-0.99964.1878-0.20770.6991-0.1068-0.06690.06410.22920.10830.4290.20160.08820.0077-0.04030.4911-0.05450.2413-27.852740.02331.355
313.32192.75241.7693.31381.88612.4128-0.3013-0.0399-0.03240.11930.24380.0519-0.07020.52460.04350.14450.03120.01540.44380.14890.2433-16.369740.864328.8271
321.0663-1.84-0.40684.1308-0.92117.7135-0.44470.11950.38650.10560.04-0.4856-1.26971.11550.39260.2957-0.1169-0.08030.25550.01510.4467-16.404254.297926.3363
332.8185-0.4789-1.02211.28540.39883.96050.11440.0226-0.4214-0.06040.229-0.37860.65881.0324-0.10440.122-0.0099-0.0480.5284-0.01060.2939-3.25937.893212.4917
341.96880.1985-1.79921.9957-0.44291.675-0.0334-0.51740.0339-0.170.18390.5776-0.38530.5601-0.17210.2341-0.1617-0.08890.4420.09760.5258-0.498946.76811.3313
356.9331-2.02663.51355.5101-3.03276.8583-0.0954-0.66320.8671-0.40230.4650.11790.1941-0.0654-0.17260.20970.05330.05970.4639-0.01860.2287-7.414744.129517.0592
368.75150.5295-0.10136.2912-0.61124.6232-0.1883-0.6245-0.88450.117-0.0067-0.25490.4471-0.6433-0.06020.1109-0.12180.12980.4719-0.05780.0767-7.873139.088417.425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 37 through 47 )C37 - 47
2X-RAY DIFFRACTION2chain 'C' and (resid 48 through 67 )C48 - 67
3X-RAY DIFFRACTION3chain 'C' and (resid 68 through 90 )C68 - 90
4X-RAY DIFFRACTION4chain 'C' and (resid 91 through 108 )C91 - 108
5X-RAY DIFFRACTION5chain 'C' and (resid 109 through 129 )C109 - 129
6X-RAY DIFFRACTION6chain 'C' and (resid 130 through 161 )C130 - 161
7X-RAY DIFFRACTION7chain 'C' and (resid 162 through 169 )C162 - 169
8X-RAY DIFFRACTION8chain 'C' and (resid 170 through 176 )C170 - 176
9X-RAY DIFFRACTION9chain 'A' and (resid 43 through 57 )A43 - 57
10X-RAY DIFFRACTION10chain 'A' and (resid 58 through 76 )A58 - 76
11X-RAY DIFFRACTION11chain 'A' and (resid 77 through 90 )A77 - 90
12X-RAY DIFFRACTION12chain 'A' and (resid 91 through 101 )A91 - 101
13X-RAY DIFFRACTION13chain 'A' and (resid 102 through 139 )A102 - 139
14X-RAY DIFFRACTION14chain 'A' and (resid 140 through 157 )A140 - 157
15X-RAY DIFFRACTION15chain 'A' and (resid 158 through 169 )A158 - 169
16X-RAY DIFFRACTION16chain 'A' and (resid 170 through 176 )A170 - 176
17X-RAY DIFFRACTION17chain 'B' and (resid 44 through 57 )B44 - 57
18X-RAY DIFFRACTION18chain 'B' and (resid 58 through 67 )B58 - 67
19X-RAY DIFFRACTION19chain 'B' and (resid 68 through 76 )B68 - 76
20X-RAY DIFFRACTION20chain 'B' and (resid 77 through 90 )B77 - 90
21X-RAY DIFFRACTION21chain 'B' and (resid 91 through 101 )B91 - 101
22X-RAY DIFFRACTION22chain 'B' and (resid 102 through 108 )B102 - 108
23X-RAY DIFFRACTION23chain 'B' and (resid 109 through 121 )B109 - 121
24X-RAY DIFFRACTION24chain 'B' and (resid 122 through 139 )B122 - 139
25X-RAY DIFFRACTION25chain 'B' and (resid 140 through 151 )B140 - 151
26X-RAY DIFFRACTION26chain 'B' and (resid 152 through 161 )B152 - 161
27X-RAY DIFFRACTION27chain 'B' and (resid 162 through 169 )B162 - 169
28X-RAY DIFFRACTION28chain 'B' and (resid 170 through 176 )B170 - 176
29X-RAY DIFFRACTION29chain 'D' and (resid 43 through 57 )D43 - 57
30X-RAY DIFFRACTION30chain 'D' and (resid 58 through 76 )D58 - 76
31X-RAY DIFFRACTION31chain 'D' and (resid 77 through 101 )D77 - 101
32X-RAY DIFFRACTION32chain 'D' and (resid 102 through 121 )D102 - 121
33X-RAY DIFFRACTION33chain 'D' and (resid 122 through 139 )D122 - 139
34X-RAY DIFFRACTION34chain 'D' and (resid 140 through 149 )D140 - 149
35X-RAY DIFFRACTION35chain 'D' and (resid 150 through 169 )D150 - 169
36X-RAY DIFFRACTION36chain 'D' and (resid 170 through 176 )D170 - 176

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