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

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Basic information

Entry
Database: PDB / ID: 8vzd
TitleCrystal Structure of 2-Hydroxyacyl-CoA lyase/synthase TbHACS from Thermoflexaceae bacterium in the Complex with THDP, Formyl-CoA and ADP
Components2-Hydroxyacyl-CoA Lyase/Synthase TbHACS
KeywordsLYASE / 2-hydroxyacyl-CoA lyase/synthase / Oxalyly-CoA decarboxylase / acyloin condensation / SBC / eBERlight
Function / homologyADENOSINE-5'-DIPHOSPHATE / Chem-FYN / DI(HYDROXYETHYL)ETHER / THIAMINE DIPHOSPHATE
Function and homology information
Biological speciesThermoflexaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: 2-Hydroxyacyl-CoA Lyase/Synthase TbHACS
B: 2-Hydroxyacyl-CoA Lyase/Synthase TbHACS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,09919
Polymers118,1202
Non-polymers3,97917
Water9,242513
1
A: 2-Hydroxyacyl-CoA Lyase/Synthase TbHACS
B: 2-Hydroxyacyl-CoA Lyase/Synthase TbHACS
hetero molecules

A: 2-Hydroxyacyl-CoA Lyase/Synthase TbHACS
B: 2-Hydroxyacyl-CoA Lyase/Synthase TbHACS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,19838
Polymers236,2404
Non-polymers7,95834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area36850 Å2
ΔGint-236 kcal/mol
Surface area62060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.173, 182.511, 123.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-Hydroxyacyl-CoA Lyase/Synthase TbHACS


Mass: 59059.953 Da / Num. of mol.: 2
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 , 7 types, 530 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FYN / S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL} THIOFORMATE


Mass: 795.544 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H36N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM Calcium Chloride, 0.1 M MES 6.0, 45 % (v/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0328 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0328 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 56818 / % possible obs: 98.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 21.57 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.081 / Rrim(I) all: 0.247 / Net I/σ(I): 6.75
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1 / Num. unique obs: 2390 / CC1/2: 0.576 / Rpim(I) all: 0.404 / Rrim(I) all: 0.798 / % possible all: 83.7

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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: 2.2→37.38 Å / SU ML: 0.2673 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.0549
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 2797 4.93 %
Rwork0.1975 53986 -
obs0.1993 56783 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8287 0 245 513 9045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00178762
X-RAY DIFFRACTIONf_angle_d0.561311948
X-RAY DIFFRACTIONf_chiral_restr0.04541285
X-RAY DIFFRACTIONf_plane_restr0.0041557
X-RAY DIFFRACTIONf_dihedral_angle_d13.06753210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.31841270.2962240X-RAY DIFFRACTION83.08
2.24-2.280.33551270.28152490X-RAY DIFFRACTION90.18
2.28-2.320.31271340.27592593X-RAY DIFFRACTION96.29
2.32-2.370.31711620.25952702X-RAY DIFFRACTION99.2
2.37-2.420.2681170.25142760X-RAY DIFFRACTION99.93
2.42-2.480.30241240.24262724X-RAY DIFFRACTION99.82
2.48-2.540.23791410.23232732X-RAY DIFFRACTION99.86
2.54-2.610.26591460.22262715X-RAY DIFFRACTION99.93
2.61-2.680.26671390.22312721X-RAY DIFFRACTION99.97
2.68-2.770.25341630.21182696X-RAY DIFFRACTION100
2.77-2.870.28911480.21582748X-RAY DIFFRACTION99.97
2.87-2.980.28231280.20962755X-RAY DIFFRACTION100
2.98-3.120.23611480.20332725X-RAY DIFFRACTION100
3.12-3.280.2411400.20392752X-RAY DIFFRACTION99.93
3.29-3.490.20651190.18482783X-RAY DIFFRACTION99.83
3.49-3.760.23471290.17322770X-RAY DIFFRACTION99.66
3.76-4.140.19921290.15862778X-RAY DIFFRACTION99.45
4.14-4.740.17041440.14472752X-RAY DIFFRACTION98.94
4.74-5.960.17891600.15772748X-RAY DIFFRACTION98.51
5.96-37.380.17491720.1532802X-RAY DIFFRACTION96.62
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)
12.25437357182-1.14696907847-0.3357751426291.593059421710.2797342213710.924763834841-0.0212919347180.01596881858580.2730240205960.05591768417960.0746352104018-0.408553964219-0.0702817822140.1404269992280.01315247767890.162690177984-0.0258492251688-0.04320808033950.208972492535-0.02210064358020.24668273082123.415634800340.109752878936.7831920731
20.387895054809-0.4738012304120.001799012950860.525352236788-0.003739716451750.633066741639-0.005409916334140.02840572484080.00542295539648-0.0503455086315-0.0259941762194-0.0595397594090.0261789366015-0.0002180541002290.04405815882180.119697771925-0.02717365841970.001829669434130.119415118440.007343642775910.14255059855813.196743496136.088768365732.4299970745
30.0381182384868-0.0718579556078-0.1243468844320.1866224696770.1269843699820.7174493421710.02671297442330.0682339258065-0.0405127330047-0.0181165835720.0296052475113-0.014813661046-0.001664773443430.221848898647-0.05132362278740.141645331823-0.03418956924260.01661072104720.202196323683-0.02409414583750.16506926513220.326595530131.32141864639.3230415344
40.445451534711-0.228852170484-0.1502936938750.826221103393-0.3926679857970.6011388150610.05845262226830.08298679574230.0166930145899-0.0255290494465-0.0299421562411-0.0208498366255-0.01384494149-0.00564101731157-0.03233827599310.168423662114-0.0100419762438-0.001221723891260.18253322786-0.001301065850060.1621441552647.5491727759136.570587647-1.18520823591
50.460458248121-0.0991717290541-0.1594615413610.4524591760940.409302299540.4797308780940.01795984485220.1035655163120.0428550215594-0.1912331742720.0002641146064580.033720608301-0.134774484568-0.111150064356-0.01042500892840.230029058714-0.00984897440618-0.02720778865760.1929404343130.04149102487240.16586890271110.392935205643.5636863236-9.69002545597
60.449768541506-0.05163019410890.1798438799280.3360019579760.112383812890.6698140238840.0503784588130.08044384666790.000400165502780.00589091001946-0.0277732368261-0.0347506129623-0.09033722146870.00835982676189-0.03458183133780.138836807319-0.01067103136350.009295428181640.144985826228-0.0001875202906930.1394181452886.5013409751856.072609321514.7553256661
70.8792755872350.3197352155620.262757064730.7573875874120.3705982519750.744759701433-0.09600148317030.1254652501630.073933310602-0.20331121277-0.001347850562610.126086186192-0.118509960595-0.06295112307660.01237929430550.2657796663720.04500666641-0.02427146695990.191941381747-0.02059255234920.215540381276-11.052030613661.555607851623.3575095025
80.69020608655-0.429319736889-0.006455647731330.707918573698-0.1471838502780.7135499349240.1033468478580.08125835706510.0375836503477-0.0711195094399-0.008639630012540.05585954523230.0509498663233-0.0899142124877-0.1052834666560.200122157317-0.00478015384368-0.01558637039760.1760329504790.01705489847270.152669271473-0.059411080906262.395868615213.0600336895
91.109800041970.194160492932-0.2167644764331.03096705271-0.9200053941861.70047355721-0.1525057756150.158282783297-0.143495050111-0.3929108397420.02701285076130.1156003296690.425157000732-0.1169681631880.1232985139820.2309911165530.0127261563485-0.01948066915210.221091941908-0.0277592383150.192650772491-7.950388271546.595499191389.19638108515
100.9099410248050.0881344017837-0.02362894905920.339303667546-0.07574488906710.165904591906-0.04032233527950.00505918346934-0.0375564548699-0.04481325697630.01988828409-0.02162813800750.02620027086310.009179957390120.01597011746680.1929541699780.001630204402120.01638405492860.147925508448-0.000408047798330.1350297245868.5891484699910.431496142115.3715246083
110.635685903270.354461277548-0.1910178668440.644466116027-0.1724014076810.846179028959-0.00496553866578-0.0411665484182-0.025260528910.0174646950603-0.022501384689-0.05568724245620.03951017445560.03063357291260.02186617960540.1403038421160.00257290080522-0.001657503013460.16458601599-0.001918314073890.19768361306831.955777778115.25393218917.6024086819
120.1950290180820.014499481442-0.04310248497440.604790923327-0.0280761078120.187576004557-0.02882006812360.0350166588598-0.0216297884560.01388152480220.0250108762848-0.07270011528740.008050903874560.01560142200990.007214916982280.1708316524190.0152990338795-0.001302392648630.1620679235970.003787126392810.16993865166819.494717623-8.5264443786822.8827487179
130.806172205776-0.169231513509-0.1621852418751.100642525160.3772862980360.945449800592-0.0366339860529-0.0901732610675-0.02490194882750.2128032294770.0037197689829-0.03774418008880.1689611838540.05492241177250.0251638196340.1699865540660.00372226684054-0.004576010048540.1277874113420.0223841850190.18244830493814.2707292759-15.538653437933.2634504186
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 30 )AA1 - 301 - 30
22chain 'A' and (resid 31 through 166 )AA31 - 16631 - 166
33chain 'A' and (resid 167 through 219 )AA167 - 219167 - 219
44chain 'A' and (resid 220 through 314 )AA220 - 314220 - 314
55chain 'A' and (resid 315 through 359 )AA315 - 359315 - 359
66chain 'A' and (resid 360 through 467 )AA360 - 467360 - 467
77chain 'A' and (resid 468 through 500 )AA468 - 500468 - 500
88chain 'A' and (resid 501 through 550 )AA501 - 550501 - 550
99chain 'B' and (resid 2 through 30 )BK2 - 301 - 29
1010chain 'B' and (resid 31 through 262 )BK31 - 26230 - 261
1111chain 'B' and (resid 263 through 337 )BK263 - 337262 - 336
1212chain 'B' and (resid 338 through 467 )BK338 - 467337 - 466
1313chain 'B' and (resid 468 through 549 )BK468 - 549467 - 548

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