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- PDB-6xn8: Crystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospi... -

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Basic information

Entry
Database: PDB / ID: 6xn8
TitleCrystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospirillales bacterium URHD0017
Components2-hydroxyacyl-CoA lyase 1
KeywordsLYASE / 2-hydroxyacyl CoA lyase / HACL / acyloin condensation / thiamine pyrophosphate
Function / homology
Function and homology information


thiamine pyrophosphate binding / lyase activity / magnesium ion binding
Similarity search - Function
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 / Chem-TZD / Unknown ligand / 2-hydroxyacyl-CoA lyase 1
Similarity search - Component
Biological speciesRhodospirillales bacterium URHD0017 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsMiller, M.D. / Xu, W. / Olmos Jr., J.L. / Chou, A. / Clomburg, J.M. / Gonzalez, R. / Philips Jr., G.N.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)STC 1231306 United States
National Science Foundation (NSF, United States)CBET-1605999 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115261 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA217255 United States
National Science Foundation (NSF, United States)GRFP 1450681 United States
CitationJournal: To Be Published
Title: Crystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospirillales bacterium URHD0017
Authors: Chou, A. / Miller, M.D. / Olmos Jr., J.L. / Xu, W. / Clomburg, J.M. / Gonzalez, R. / Philips Jr., G.N.
History
DepositionJul 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-hydroxyacyl-CoA lyase 1
B: 2-hydroxyacyl-CoA lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,05510
Polymers118,2712
Non-polymers1,7848
Water22,5551252
1
A: 2-hydroxyacyl-CoA lyase 1
B: 2-hydroxyacyl-CoA lyase 1
hetero molecules

A: 2-hydroxyacyl-CoA lyase 1
B: 2-hydroxyacyl-CoA lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,11020
Polymers236,5434
Non-polymers3,56716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area28490 Å2
ΔGint-215 kcal/mol
Surface area64840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.940, 64.431, 182.693
Angle α, β, γ (deg.)90.000, 90.880, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-1264-

HOH

21B-1275-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 184 or resid 186...
21(chain B and (resid 2 through 184 or resid 186...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPRO(chain A and (resid 2 through 184 or resid 186...AA2 - 1842 - 184
12SERSERGLYGLY(chain A and (resid 2 through 184 or resid 186...AA186 - 315186 - 315
13ALAALAARGARG(chain A and (resid 2 through 184 or resid 186...AA317 - 329317 - 329
14TRPTRPPROPRO(chain A and (resid 2 through 184 or resid 186...AA331 - 379331 - 379
15ASNASNPROPRO(chain A and (resid 2 through 184 or resid 186...AA381 - 479381 - 479
16ASNASNLEULEU(chain A and (resid 2 through 184 or resid 186...AA481 - 486481 - 486
17PROPROASPASP(chain A and (resid 2 through 184 or resid 186...AA488 - 498488 - 498
18VALVALVALVAL(chain A and (resid 2 through 184 or resid 186...AA500 - 511500 - 511
19GLUGLUPHEPHE(chain A and (resid 2 through 184 or resid 186...AA513 - 527513 - 527
110GLYGLYGLYGLY(chain A and (resid 2 through 184 or resid 186...AA529 - 540529 - 540
21SERSERPROPRO(chain B and (resid 2 through 184 or resid 186...BB2 - 1842 - 184
22SERSERGLYGLY(chain B and (resid 2 through 184 or resid 186...BB186 - 315186 - 315
23ALAALAARGARG(chain B and (resid 2 through 184 or resid 186...BB317 - 329317 - 329
24TRPTRPPROPRO(chain B and (resid 2 through 184 or resid 186...BB331 - 379331 - 379
25ASNASNPROPRO(chain B and (resid 2 through 184 or resid 186...BB381 - 479381 - 479
26ASNASNLEULEU(chain B and (resid 2 through 184 or resid 186...BB481 - 486481 - 486
27PROPROASPASP(chain B and (resid 2 through 184 or resid 186...BB488 - 498488 - 498
28VALVALVALVAL(chain B and (resid 2 through 184 or resid 186...BB500 - 511500 - 511
29GLUGLUPHEPHE(chain B and (resid 2 through 184 or resid 186...BB513 - 527513 - 527
210GLYGLYGLYGLY(chain B and (resid 2 through 184 or resid 186...BB529 - 540529 - 540

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-hydroxyacyl-CoA lyase 1


Mass: 59135.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: codon optimized synthetic gene
Source: (gene. exp.) Rhodospirillales bacterium URHD0017 (bacteria)
Gene: SAMN02990966_07839 / Plasmid: pNIC28-Bsa4-RuHACL / Details (production host): TEV-cleavable N-terminal HIS-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1H8YFL8

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Non-polymers , 5 types, 1260 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1252 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% (w/v) SOKALAN PA 25 CL, 0.1 M HEPES, pH 7, 0.1 M sodium chloride. ADDITIVE: 0.002 M thiamine diphosphate, 0.02 M CoA-SH, 0.002 M magnesium chloride, 0.002 M ADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→52.93 Å / Num. obs: 67457 / % possible obs: 76.4 % / Redundancy: 2.96 % / Biso Wilson estimate: 10.8 Å2
Details: Data were elliptically truncated with STARANISO. Statistics reported are for the observed reflections in spherical shells after appling the elliptical observation criterion.
CC1/2: 0.958 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.151 / Rrim(I) all: 0.267 / Net I/σ(I): 3.635 / Num. measured all: 195348
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-2.0362.310.752725733740.4530.6040.971.28631.25
5.839-52.932.920.091964033730.9850.0630.1116.3298.45

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: AWSEM-suite model generated using 5dx6 as the template

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.17.1_3660refinement
ARP/wARP8.0 patch 1model building
PHASERphasing
Aimless0.7.4data scaling
DIALS1.14.5-g19190e3b9-releasedata reduction
xia20.5.893-gb176367e-dials-1.14data reduction
JBluIce-EPICSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dx6

5dx6


Resolution: 1.95→45.47 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.57 / Stereochemistry target values: ML
Details: 1. DATA WAS ANIOSTROPICALLY TRUNCATED WITH STARANISO. 2. ELECTRON DENSITY SUPPORTS MODELING THE DENSITY IN THE THIAMIN DIPHOSPHATE BINDING SITE AS THE THIAZOLONE DERIVATIVE -- THIAMIN 2- ...Details: 1. DATA WAS ANIOSTROPICALLY TRUNCATED WITH STARANISO. 2. ELECTRON DENSITY SUPPORTS MODELING THE DENSITY IN THE THIAMIN DIPHOSPHATE BINDING SITE AS THE THIAZOLONE DERIVATIVE -- THIAMIN 2-THIAZOLONE DIPHOSPHATE. 3. THE NOMINAL RESOLUTION USING THE 100% CRITERION IS 2.15 A WITH 8569 REFLECTIONS BETWEEN 2.15-1.95 A INCLUDED IN REFINEMENT (39% FOR THIS SHELL). 4. AN UNKNOWN LIGAND (UNL) WAS MODELED INTO DENSITY FOUND IN THE TETRAMER INTERFACE. ITS SHAPE IS SIMILAR TO BENZOATE, NITROBENZENE AND NIACIN.
RfactorNum. reflection% reflection
Rfree0.212 3563 5.28 %
Rwork0.1858 63861 -
obs0.1872 67424 76.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.3 Å2 / Biso mean: 14.1313 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.95→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8095 0 182 134 8411
Biso mean--9.83 15.85 -
Num. residues----1079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038471
X-RAY DIFFRACTIONf_angle_d0.62711518
X-RAY DIFFRACTIONf_chiral_restr0.0441259
X-RAY DIFFRACTIONf_plane_restr0.0041573
X-RAY DIFFRACTIONf_dihedral_angle_d16.6273176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.980.2997450.264188192626
1.98-20.2848550.25531062111732
2-2.030.3232610.2541181124236
2.03-2.070.2922730.2431334140740
2.07-2.10.2892840.23571502158645
2.1-2.140.3018960.23011701179751
2.14-2.170.26341070.22331918202557
2.17-2.220.24561040.21452138224263
2.22-2.260.25181360.22492254239068
2.26-2.310.27961450.21172431257672
2.31-2.360.22751500.20942563271378
2.36-2.420.24271480.20632714286282
2.42-2.490.2261610.20622873303485
2.49-2.560.23971810.19552905308688
2.56-2.650.25411570.19363106326392
2.65-2.740.23691780.19973180335896
2.74-2.850.22081670.1983306347398
2.85-2.980.18292010.19113306350799
2.98-3.140.20512140.18573287350199
3.14-3.330.20651920.177133453537100
3.33-3.590.18931890.15653347353699
3.59-3.950.16711890.14323333352299
3.95-4.520.15251520.13323398355099
4.52-5.70.15512010.14943355355699
5.7-45.470.18751770.19793441361898

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