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- PDB-8vzk: Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase CfhHACS fro... -

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Basic information

Entry
Database: PDB / ID: 8vzk
TitleCrystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase CfhHACS from Chloroflexi bacterium in the Complex with THDP and ADP
ComponentsOxalyl-CoA decarboxylase
KeywordsLYASE / 2-hydroxyacyl-CoA lyase/synthase / Oxalyly-CoA decarboxylase / acyloin condensation / Structural Biology Center / eBERlight
Function / homology
Function and homology information


oxalyl-CoA decarboxylase / oxalyl-CoA decarboxylase activity / fatty acid alpha-oxidation / thiamine pyrophosphate binding / peroxisome / magnesium ion binding
Similarity search - Function
TPP-binding domain containing protein HACL1-like / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / THIAMINE DIPHOSPHATE / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesChloroflexi bacterium HGW-Chloroflexi-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKim, Y. / Gade, P. / Mayfield, A. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,57512
Polymers120,5292
Non-polymers2,04610
Water724
1
A: Oxalyl-CoA decarboxylase
B: Oxalyl-CoA decarboxylase
hetero molecules

A: Oxalyl-CoA decarboxylase
B: Oxalyl-CoA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,15024
Polymers241,0594
Non-polymers4,09220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area28080 Å2
ΔGint-199 kcal/mol
Surface area62600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.327, 111.327, 193.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Oxalyl-CoA decarboxylase


Mass: 60264.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexi bacterium HGW-Chloroflexi-9 (bacteria)
Gene: CVU47_07430 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A2N2LHX4, oxalyl-CoA decarboxylase

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Non-polymers , 6 types, 14 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-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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 magnesium chloride, 0.1 M hepes pH 7.5, 30 % (v/v) PEG400

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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 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 39660 / % possible obs: 97.1 % / Redundancy: 14.2 % / Biso Wilson estimate: 59.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.168 / Net I/σ(I): 13
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 1 / Num. unique obs: 1347 / CC1/2: 0.837 / Rrim(I) all: 0.952 / % possible all: 68.4

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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: 2.65→48.23 Å / SU ML: 0.3997 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.5897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2444 1913 4.85 %
Rwork0.2118 37562 -
obs0.2134 39475 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.22 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8209 0 127 4 8340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00178510
X-RAY DIFFRACTIONf_angle_d0.484911567
X-RAY DIFFRACTIONf_chiral_restr0.04241268
X-RAY DIFFRACTIONf_plane_restr0.00421519
X-RAY DIFFRACTIONf_dihedral_angle_d12.17553118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.3639890.37061889X-RAY DIFFRACTION69.11
2.72-2.790.3691100.37672392X-RAY DIFFRACTION87.57
2.79-2.870.3761200.35092704X-RAY DIFFRACTION97.92
2.87-2.970.33911100.32772764X-RAY DIFFRACTION99.76
2.97-3.070.36291510.29922718X-RAY DIFFRACTION99.65
3.07-3.190.34921360.2922744X-RAY DIFFRACTION99.65
3.19-3.340.27551260.27622738X-RAY DIFFRACTION99.69
3.34-3.520.25571630.22822729X-RAY DIFFRACTION99.55
3.52-3.740.24191540.21762782X-RAY DIFFRACTION99.8
3.74-4.020.23571410.19082751X-RAY DIFFRACTION99.83
4.02-4.430.22391550.17882771X-RAY DIFFRACTION99.76
4.43-5.070.19251530.16142810X-RAY DIFFRACTION99.83
5.07-6.390.22421420.19012829X-RAY DIFFRACTION100
6.39-48.230.19061630.15072941X-RAY DIFFRACTION99.61
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)
10.586329561764-0.263333739249-0.1754981010391.309385174340.1802790328881.44517172505-0.01382188220360.0394382000975-0.1152083773070.0881283179817-0.09780076433250.1350393232760.345159544534-0.07800930702640.09706790537110.509264929054-0.09148117232640.06420020414820.690401769736-0.01075366321810.34943544887549.1404281576-17.8623604963-20.5451527488
22.277570741520.7373945964370.4924048661213.404594224980.2079253476712.80964200459-0.547298330386-0.116569899030.0327366885184-0.3597896700350.099204060242-0.293879601020.5569374209050.6294646689130.1911246682790.6277370712960.1140635613320.1496637948910.8533692683650.02843319524480.44382560071970.1145954802-26.8622391187-29.6285461603
34.37188743920.4917619616763.194863690322.10563561850.1444076441133.382829017530.24137762172-0.241111669986-0.6134287746710.139096949869-0.033592166512-0.2920688881010.7848128028890.144072622526-0.2379008595190.9343567496680.09455350888850.1572734089850.7889721624810.1461371097360.53245883851172.5259433309-39.8549339755-16.1361546545
42.903637189040.222748554054-2.337676639385.71657720342-0.3717411089142.10695368817-0.027152262004-0.358238918768-0.3768749676020.522267200499-0.100991563944-0.6359747873630.3760656472430.8229056140420.188742520970.8472159730480.0772729687967-0.04910046348270.8611339065370.08195748606440.39606847088366.9743668928-22.34767595252.22514726196
50.738562503344-0.7143314713390.2290878195931.861655902680.6955638042941.55814891819-0.244084408708-0.109139707197-0.1347266047430.3919122553220.03186889597270.1365579703740.1746681791730.1528970044320.2349699101690.672861474573-0.02808853834230.07946179700290.7495971346730.05076818875660.43338215830654.6919992215-17.4156380916-4.48257757284
61.02234289253-0.6859871211070.01644691810361.90817928316-0.4230312178261.84664575181-0.0633741941954-0.1906087241760.02218144205160.759033219144-0.00858713478505-0.435459692183-0.02508693607620.6067171456090.1429570483160.7996177475-0.0701194175355-0.02338489183930.8845135350310.01841909516910.39695462997866.2158099913-5.275995462963.64732747063
71.14849729192-1.07875806037-0.2344967329022.16732609370.3560576899911.50003299933-0.128536265697-0.429547353991-0.1499147578150.507350636757-0.0543520119431-0.07598801556590.1627672632740.3074224813750.048686619170.960909569134-0.08973566805020.06547598860030.8880703004390.09426618620430.48580677435561.1980397871-15.84250908979.4222780471
81.016475875830.696981092076-0.0648845474262.372864558640.312638776761.20166478813-0.1086028351030.1113376471260.03322526210890.5977982468570.0147830134318-0.578435942034-0.1872217135040.883656746637-0.03207454891630.482158249667-0.167720756911-0.0829015084670.8330793541760.07690723766810.45185746825374.47518086738.94035442665-14.8359079479
90.3681020287710.04409929230010.04014175747741.607351320520.8036366914261.263788192530.0301050435076-0.0324404815545-0.01135084731440.16285601035-0.183377669062-0.157483650123-0.0134843943260.2627648350740.121457160370.423054962707-0.0803590200468-0.03586285661750.7694767016320.05479860490380.34495827213264.25303727476.02390175795-18.7938398543
100.861429739495-0.3702427695630.3621368372141.882755474560.6823193952811.47782462978-0.003380886252660.2299343341770.0584028411158-0.0343401644804-0.0164428843423-0.322969489389-0.2650939179470.2851600454340.04897653258380.479550425271-0.079382447010.0013980689950.8409974744430.0493548564960.44253971283570.060582223815.1284738847-23.6887017598
112.693523016090.295992659182-0.8847643376462.80557562844-0.1007338790822.332381906940.118179093687-0.2664293105790.1847735886140.334907454549-0.1612234716590.3256849135-0.7343277767110.1129484220040.08970351596790.8176418535210.0901366161715-0.03760682150310.808179986177-0.08856612227120.41534642154740.947701584233.4860708677-13.1017618655
122.343458283210.179657713354-0.9544756908213.010644503060.3757645569032.35523877876-0.1924198938990.461520286427-0.0752216661756-0.266920333044-0.1113635304580.484208300527-0.490881596837-0.6109971063610.229229234860.6277479513440.105653722333-0.05585480185060.863980155862-0.03874760617360.53989343036235.586396792625.0822823856-21.4207045467
132.297520324490.0807353871492-0.8662221100871.95325751273-1.202255067862.579368450620.154327837839-0.306602607530.4138932904110.531782410755-0.1092181409390.429826558569-0.792466110697-0.364609128040.002565561935471.057401814540.106258839099-0.03366117690180.948772265599-0.2572288634890.72321093979234.495784998336.0538140891-8.71594541402
143.792462046561.368333915350.3943532352514.371176943010.6848129611561.42590387244-0.083237838844-0.1263852015020.4074608169430.695631551546-0.03464056316730.41107528689-0.689639698465-0.4472616833920.09569896446390.8715126520640.0311274133780.03542601190310.853910490977-0.0692766744020.45210798703440.61092126215.93578754875.43822950387
150.47900829278-0.3057209436-0.4441931420451.309650473970.264409334162.098977120370.0384660223043-0.1588111771370.09327460521970.542383095936-0.06036762800760.01424836059650.202346753407-0.08326855712660.06218176245860.777037262168-0.0865321210423-0.001714184260260.755866410416-0.02258895306680.39225063541252.542491135312.3502011224-1.85262911769
161.93319185239-0.389737560228-0.74775383011.8128502977-0.1523528392853.12659288687-0.175941708863-0.383035124454-0.1678922129330.624377302120.05366149103420.3813305239610.259464278134-0.5694829679130.172317430910.795039915261-0.121039934330.09297588347570.930597310974-0.01221875897970.42612633082341.0530264902-0.9576638003694.04433489829
171.45957486233-0.854929117486-0.4238264038731.86031761055-0.7573017260921.81160764256-0.11636256683-0.299064854393-0.06698382271680.6490195104430.05136440018430.203852723282-0.527426877997-0.1109882337860.04548045800791.10622686509-0.02906942106710.05317312415620.888630150068-0.05840502860930.43592393210346.08184698118.4008039612811.6504649466
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 287 )AA8 - 2871 - 280
22chain 'A' and (resid 288 through 321 )AA288 - 321281 - 314
33chain 'A' and (resid 322 through 365 )AA322 - 365315 - 358
44chain 'A' and (resid 366 through 405 )AA366 - 405359 - 398
55chain 'A' and (resid 406 through 463 )AA406 - 463399 - 456
66chain 'A' and (resid 464 through 501 )AA464 - 501457 - 494
77chain 'A' and (resid 502 through 550 )AA502 - 550495 - 543
88chain 'B' and (resid 9 through 37 )BH9 - 371 - 29
99chain 'B' and (resid 38 through 156 )BH38 - 15630 - 148
1010chain 'B' and (resid 157 through 196 )BH157 - 196149 - 188
1111chain 'B' and (resid 197 through 262 )BH197 - 262189 - 254
1212chain 'B' and (resid 263 through 321 )BH263 - 321255 - 313
1313chain 'B' and (resid 322 through 366 )BH322 - 366314 - 358
1414chain 'B' and (resid 367 through 405 )BH367 - 405359 - 397
1515chain 'B' and (resid 406 through 463 )BH406 - 463398 - 455
1616chain 'B' and (resid 464 through 501 )BH464 - 501456 - 493
1717chain 'B' and (resid 502 through 550 )BH502 - 550494 - 542

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