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- PDB-8vzh: Crystal Structure of 2-Hydroxyacyl-CoA lyase/synthase TbHACS from... -

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Basic information

Entry
Database: PDB / ID: 8vzh
TitleCrystal Structure of 2-Hydroxyacyl-CoA lyase/synthase TbHACS from Thermoflexaceae bacterium in the Complex with THDP and ADP
ComponentsOxalyl-CoA decarboxylase
KeywordsLYASE / 2-hydroxyacyl-CoA lyase/synthase / Oxalyly-CoA decarboxylase / acyloin condensation / SBC / eBERlight
Function / homologyADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesThermoflexaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKim, Y. / Maltseva, M. / Endres, M. / Lee, S. / Yoshikuni, Y. / Gonzalez, R. / Michalska, K. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Commun Chem / Year: 2024
Title: Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family.
Authors: Kim, Y. / Lee, S.H. / Gade, P. / Nattermann, M. / Maltseva, N. / Endres, M. / Chen, J. / Wichmann, P. / Hu, Y. / Marchal, D.G. / Yoshikuni, Y. / Erb, T.J. / Gonzalez, R. / Michalska, K. / Joachimiak, A.
History
DepositionFeb 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxalyl-CoA decarboxylase
B: Oxalyl-CoA decarboxylase
C: Oxalyl-CoA decarboxylase
D: Oxalyl-CoA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,17138
Polymers236,2404
Non-polymers4,93134
Water14,772820
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28930 Å2
ΔGint-237 kcal/mol
Surface area64720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.591, 134.013, 173.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Oxalyl-CoA decarboxylase


Mass: 59059.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoflexaceae bacterium (bacteria) / Plasmid: p53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold

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Non-polymers , 8 types, 854 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium/potassium phosphate, 0.1 M Bis Tris propane pH 6.5 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 133571 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 27.57 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.077 / Rrim(I) all: 0.177 / Net I/σ(I): 10.3
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 5 % / Rmerge(I) obs: 1.196 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6589 / CC1/2: 0.659 / Rpim(I) all: 0.593 / Rrim(I) all: 1.338 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→43.39 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1949 6701 5.04 %
Rwork0.1596 126194 -
obs0.1614 132895 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.47 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16212 0 297 820 17329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003816979
X-RAY DIFFRACTIONf_angle_d0.690323151
X-RAY DIFFRACTIONf_chiral_restr0.04832505
X-RAY DIFFRACTIONf_plane_restr0.00533049
X-RAY DIFFRACTIONf_dihedral_angle_d14.49176194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.270.25662070.2273715X-RAY DIFFRACTION88.47
2.27-2.30.26062230.21134086X-RAY DIFFRACTION98.38
2.3-2.330.24921920.21514070X-RAY DIFFRACTION96.47
2.33-2.360.27322180.21794115X-RAY DIFFRACTION97.52
2.36-2.390.28821920.20894182X-RAY DIFFRACTION99.18
2.39-2.420.23272300.19724178X-RAY DIFFRACTION99.98
2.42-2.460.23542220.19684211X-RAY DIFFRACTION99.82
2.46-2.490.2592230.19754190X-RAY DIFFRACTION99.91
2.49-2.530.25352400.1884193X-RAY DIFFRACTION100
2.53-2.570.22872210.18584204X-RAY DIFFRACTION100
2.57-2.620.23062090.19394195X-RAY DIFFRACTION99.91
2.62-2.660.25882450.19814190X-RAY DIFFRACTION99.91
2.66-2.720.24982060.19354220X-RAY DIFFRACTION99.95
2.72-2.770.2382090.17844233X-RAY DIFFRACTION100
2.77-2.830.21752360.1764186X-RAY DIFFRACTION99.8
2.83-2.90.21172480.18174212X-RAY DIFFRACTION99.87
2.9-2.970.21742050.17654239X-RAY DIFFRACTION100
2.97-3.050.22352330.18184213X-RAY DIFFRACTION99.87
3.05-3.140.22162110.1834209X-RAY DIFFRACTION99.82
3.14-3.240.21712230.1794232X-RAY DIFFRACTION99.87
3.24-3.360.20872220.17854251X-RAY DIFFRACTION99.93
3.36-3.490.20872370.15834206X-RAY DIFFRACTION99.89
3.49-3.650.18442220.14484245X-RAY DIFFRACTION99.8
3.65-3.840.15792320.14094276X-RAY DIFFRACTION99.87
3.84-4.080.16421940.12734274X-RAY DIFFRACTION99.98
4.08-4.40.142400.11374274X-RAY DIFFRACTION100
4.4-4.840.13342290.11124269X-RAY DIFFRACTION99.65
4.84-5.540.13562290.12094300X-RAY DIFFRACTION99.69
5.54-6.970.17712360.13994355X-RAY DIFFRACTION99.93
6.98-43.390.14782670.12984471X-RAY DIFFRACTION99.2
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7236370504720.16139202235-0.2754160776260.2298511077170.03699193855751.197705365740.0293282901901-0.02626720597970.08244546075270.02424444983660.006143625599770.0129443914284-0.0777467004696-0.0120410764211-0.02908533744530.204894663135-0.00362459652443-0.006915224577370.1394386405550.01623125015520.206406698368-13.976830170615.9948309839-12.0797494222
20.2541931870740.137438160409-0.1614022985061.208116666671.221002168072.198898103920.01131086927760.01343997080650.0925714117935-0.175059603360.076577123665-0.0602711965337-0.2673301835180.0972891348913-0.09092434083940.22173532849-0.005507448670150.01423770892580.1820596551350.01428779165720.24128295569-8.5500301916312.2985344905-35.8436498996
30.358446858525-0.0233132300518-0.05172675422480.3327053159150.2120065730710.9828474791460.004103607001550.0657651258127-0.0190975383882-0.03861824460310.0192849917684-0.0005961412567820.111188892093-0.122981931192-0.01607718601810.243994449797-0.0244193893299-0.01121139931180.17558167183-0.0007721328127120.210955530693-22.0067458323-2.63880383959-36.1374634154
41.63177366789-0.2547744003430.3898422271761.121169945850.05833338830161.284555663440.0237423424145-0.00289934008066-0.226927462884-0.08026050142570.03189668871980.0276382439680.270554024092-0.419570292815-0.05355516159820.252756306411-0.120615008955-0.0002526141898860.3013687542690.0190412480930.216903312317-40.7221983617-8.34180834575-17.4449680742
51.93550142872-0.5975847047870.1794312948871.46385578840.3982867879382.20731900687-0.0474517950422-0.228949836857-0.4231717238530.3113163658140.03544158343630.02210890914950.4020697404360.04764675643210.01695369678540.391330226041-0.03516966801570.02279010448490.1733886188270.07556393842810.314451532689-14.1625021333-22.3757060794-4.53306977242
60.81967404487-0.06987233033850.01416127671510.407713555406-0.01481343569191.837537873390.0528097074276-0.12292916418-0.157470635005-0.00126961683158-0.0742115046143-0.06497717264660.299440443472-0.09125859221230.03805961907890.317035742881-0.0456129742246-0.004248719651990.1886029463690.03515463448130.25080260588-19.7256550272-13.3573661881-1.96017646393
70.4507411740180.0904112586957-0.02453021650140.1263992648350.1137088585991.177725806730.031849145692-0.0629135620221-0.134806425195-0.0203681712217-0.0252410755465-0.1237738836490.149264617780.1543026928320.002173572021090.2852196891960.0010834302825-0.01031529986670.1750311423810.03831349750230.249401524626-7.08690610287-10.2644312535-5.81980461329
80.524150463991-0.003603939897630.02019901855110.8214558906380.5168683289321.67043174870.036472795524-0.202148728422-0.131968271450.172906518424-0.0270617794179-0.0828549396880.3452488357940.170963312534-0.02775346900520.306388238562-0.0327827557938-0.0198964913430.2919855619380.08335502392180.243012238376-6.63088375084-8.7652459217919.1351475229
91.00037224717-0.0876140495583-0.3835957915110.222472557373-0.06487094456591.519354994240.072630225737-0.140156067834-0.01742599264550.111467727727-0.0485356143805-0.008298279991780.003246628642710.0478359905945-0.01337044221780.312599371106-0.0490855478844-0.01610627593450.3211339994920.02135744704540.22412030327-12.29238903595.1512241474726.68235636
100.3730104865460.0707546141813-0.2040949036890.1525457968540.08002632569960.6964887892230.00971673731135-0.0397453518161-0.03487545069130.0661550587282-0.01652565591330.06081287840290.13843782121-0.133576474634-0.009459370831270.23735464192-0.0459999394255-0.005322265368150.2328034805540.03285996793620.184358325237-31.25284050313.3256471595313.5791968137
111.723954910310.233853729531-0.0793118359741.865491198720.1333975286761.322627323830.00418697074587-0.03531721261080.01760153448220.1247629730590.006396290768150.151001007863-0.0232920200604-0.392320614967-0.02280057196040.186548670187-0.0207657236761-8.35520764141E-50.2789216727660.01242317857280.162719135125-40.95192304825.120464286881.46849652572
120.4805795967640.06886571205430.1603270978071.21149342224-0.4599217781060.981029597764-0.008616598405080.00796920119331-0.2021390325370.0269262484290.0107180438948-0.07865936358420.1790754939130.227067440049-0.0002369082135740.2373224005540.06891735363930.0110736785750.2425416956330.006122493595550.26885419078314.4329682853-5.88094353211-20.3653634996
130.579420400947-0.2719495998050.1689893018922.51361263889-0.72882525551.032240790890.04863703781260.0770843487037-0.0436457170389-0.261942664535-0.01353595854770.02551868499370.0921568068030.106873337733-0.06188626766510.197631657833-0.001971688692380.02808885482240.210225010501-0.007234413505940.2090362368528.019109534210.455433492-36.7540375681
140.9585766326010.2272379527590.1498582791170.924160673967-0.2424051302641.243808936920.0368788858307-0.009489554839090.01683113262110.0321088937345-0.0327301555366-0.0179944553173-0.1756986740540.143824862430.002235321807210.278637752876-0.05316501633980.01015725549340.2061347776390.00559641485670.26172444459411.466804373827.2991324373-31.179855355
151.331298700440.501535828467-0.1245756663522.10471639561-0.3813965195720.725826838899-0.09160576069040.01280480422220.124033484826-0.1530162994890.0390828649238-0.133929026923-0.3741167157480.3806423217230.05714240475020.331271879233-0.09435359404210.05586191378630.3185764382340.02803543794560.24283427026317.982934951833.7616196921-38.0612614405
161.157241236690.2206436829120.08256135143240.687878441603-0.2594335563690.9890236704820.063787069944-0.1026669746220.04564343259830.0525561118555-0.0796771225025-0.28569124089-0.1603568926170.612519070916-0.006026477136870.219851966827-0.0556712831265-0.009040954376990.4983712043190.01164525201020.33828947570735.714521373416.2949745681-18.0811682327
171.4030394865-0.159666394353-0.1604864607170.969768521894-0.3104679500161.135864222640.074066618497-0.3175781870190.0107872950010.13515812058-0.0539042798659-0.17201647763-0.1140817897170.396233369952-0.03716042720010.197643906603-0.050080024923-0.07186395462960.34938853392-0.005727235684840.22895382593119.073327762115.00985183856.61511340356
180.3282327162030.202827737632-0.2127756774750.343822851288-0.3130365399030.764387960890.018666612967-0.09249386822510.03884404743360.04269443728010.01244696560870.00568778897162-0.00555928906110.146354024876-0.02291620151250.217904534907-0.014668928024-0.04024565267060.2612423476660.01391315225220.2404707748568.3465476376111.20012190360.835684371854
190.5178296974590.0772291289966-0.1904719235331.86780436927-0.4014221335910.9360071485280.044890520729-0.176623071686-0.1642994743250.352076880203-0.142274780289-0.08209693437180.1183035028360.270892951410.09331711963580.3227566538280.029695647668-0.06350120247890.3282959637950.08170652774320.2471137096829.40997404251-4.7157502668519.8682728208
200.977859753252-0.226192698604-0.1937573589950.462756430103-0.315580089350.4454146912860.0437213390861-0.237221747462-0.1274373088090.0716264457649-0.0469900218211-0.111861504410.3602184491720.3752530915130.04325747749860.4443755662180.146293907896-0.08051216180340.4422009464070.1571059698470.42130105981220.0061263594-20.005681479615.8306043669
211.26625689034-0.2663935087720.09037953368781.36369473251-0.09703626322590.842878337932-0.056782088214-0.242510505376-0.2469947370960.03809666251310.0418163052332-0.06629245407650.3817979750.198413044388-0.02330030295640.4353804330760.0866898752127-0.05996074294060.3397077175530.1365037046620.3853471845879.87096387945-21.312800954518.6930117707
220.563505726867-0.0152162945905-0.01421462008060.323919845205-0.3244927053680.4776130780180.000397068144343-0.108253150675-0.1695643146540.097790239769-0.0921901365834-0.2761036928680.2415259620430.5068953068170.09176003319750.355928111270.14271189824-0.08654204450320.5790316732030.1032500898250.43585261977433.7368073134-9.961367304166.40895074391
231.456205437180.2423511580350.7632682653961.356187240480.1832241351621.310197706790.0588475624463-0.00128637789836-0.2080229558360.0545747606649-0.0519309434106-0.3089496907350.2629801343490.676038362742-0.002264646375620.287275153470.119222499541-0.01954732781330.7233129363420.06729878577740.46433391106243.1297081245-5.8850852252-5.87593533443
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 166 )AA1 - 1661 - 166
22chain 'A' and (resid 167 through 219 )AA167 - 219167 - 219
33chain 'A' and (resid 220 through 467 )AA220 - 467220 - 467
44chain 'A' and (resid 468 through 539 )AA468 - 539468 - 539
55chain 'B' and (resid 1 through 30 )BH1 - 301 - 30
66chain 'B' and (resid 31 through 75 )BH31 - 7531 - 75
77chain 'B' and (resid 76 through 166 )BH76 - 16676 - 166
88chain 'B' and (resid 167 through 219 )BH167 - 219167 - 219
99chain 'B' and (resid 220 through 337 )BH220 - 337220 - 337
1010chain 'B' and (resid 338 through 456 )BH338 - 456338 - 456
1111chain 'B' and (resid 457 through 539 )BH457 - 539457 - 539
1212chain 'C' and (resid 1 through 166 )CN1 - 1661 - 166
1313chain 'C' and (resid 167 through 219 )CN167 - 219167 - 219
1414chain 'C' and (resid 220 through 314 )CN220 - 314220 - 314
1515chain 'C' and (resid 315 through 359 )CN315 - 359315 - 359
1616chain 'C' and (resid 360 through 539 )CN360 - 539360 - 539
1717chain 'D' and (resid 1 through 75 )DT1 - 751 - 75
1818chain 'D' and (resid 76 through 166 )DT76 - 16676 - 166
1919chain 'D' and (resid 167 through 219 )DT167 - 219167 - 219
2020chain 'D' and (resid 220 through 280 )DT220 - 280220 - 280
2121chain 'D' and (resid 281 through 337 )DT281 - 337281 - 337
2222chain 'D' and (resid 338 through 467 )DT338 - 467338 - 467
2323chain 'D' and (resid 468 through 539 )DT468 - 539468 - 539

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