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

ID or keywords:

Entry

Database: PDB / ID: 8vze

Title

Crystal Structure of 2-Hydroxyacyl-CoA lyase/synthase TbHACS from Thermoflexaceae bacterium in the Complex with THDP, 2-Hydroxyisobutyryl-CoA and ADP

Components

Oxalyl-CoA decarboxylase

Keywords

LYASE / 2-hydroxyacyl-CoA lyase/synthase / Oxalyly-CoA decarboxylase / acyloin condensation / SBC / eBERlight

Function / homology

: / ADENOSINE-5'-DIPHOSPHATE / COENZYME A

Function and homology information

Biological species

Thermoflexaceae bacterium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.69 Å

Authors

Kim, Y. / Maltseva, M. / Endres, M. / Lee, S. / Yoshikuni, Y. / Gonzalez, R. / Michalska, K. / Joachimiak, A.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Feb 11, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vze.cif.gz	497.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8vze.ent.gz		Display	PDB format
PDBx/mmJSON format	8vze.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vze_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8vze_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8vze_validation.xml.gz	54.9 KB	Display
Data in CIF	8vze_validation.cif.gz	78.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/8vze ftp://data.pdbj.org/pub/pdb/validation_reports/vz/8vze	HTTPS FTP

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Related structure data

Related structure data	8vzaC 8vzbC 8vzcC 8vzdC 8vzfC 8vzhC 8vziC 8vzjC 8vzkC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Oxalyl-CoA decarboxylase

B: Oxalyl-CoA decarboxylase

hetero molecules

122 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Oxalyl-CoA decarboxylase

B: Oxalyl-CoA decarboxylase

hetero molecules

A: Oxalyl-CoA decarboxylase

B: Oxalyl-CoA decarboxylase

hetero molecules

defined by author&software
244 kDa, 4 polymers

Unit cell

Length a, b, c (Å)	100.621, 182.770, 123.844
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
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

Components on special symmetry positions

ID	Model	Components
1	1	A-750- HOH
2	1	A-973- HOH
3	1	A-1110- HOH
4	1	B-937- HOH
5	1	B-979- HOH
6	1	B-1057- HOH
7	1	B-1095- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Oxalyl-CoA decarboxylase 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 , 6 types, 950 molecules

#2: Chemical	ChemComp-A1AEK / 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(hydroxymethyl)-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium Mass: 455.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₂₁N₄O₈P₂S
#3: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 936 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.08 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 20 % (w/v) PEG 10000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.69→50 Å / Num. obs: 123996 / % possible obs: 98.3 % / Redundancy: 8 % / B_iso Wilson estimate: 14.91 Å² / CC_1/2: 0.984 / R_merge(I) obs: 0.188 / R_pim(I) all: 0.068 / R_rim(I) all: 0.201 / Net I/σ(I): 14.06
Reflection shell	Resolution: 1.69→1.73 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.85 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 5095 / CC_1/2: 0.506 / R_pim(I) all: 0.465 / R_rim(I) all: 0.977 / % possible all: 81.4

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.69→48.04 Å / SU ML: 0.1437 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1743	6044	4.91 %
R_work	0.1453	117122	-
obs	0.1468	123166	97.56 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 17.56 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→48.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8307	0	201	936	9444

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0109	8855
X-RAY DIFFRACTION	f_angle_d	1.136	12098
X-RAY DIFFRACTION	f_chiral_restr	0.0714	1297
X-RAY DIFFRACTION	f_plane_restr	0.0114	1589
X-RAY DIFFRACTION	f_dihedral_angle_d	16.1727	3292

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.69-1.71	0.2539	130	0.221	2664	X-RAY DIFFRACTION	66.59
1.71-1.73	0.1945	168	0.19	3340	X-RAY DIFFRACTION	84.08
1.73-1.75	0.2343	168	0.1878	3531	X-RAY DIFFRACTION	88.81
1.75-1.78	0.2392	165	0.1841	3702	X-RAY DIFFRACTION	92.82
1.78-1.8	0.1932	183	0.1801	3856	X-RAY DIFFRACTION	96.67
1.8-1.83	0.2274	188	0.182	3952	X-RAY DIFFRACTION	99.54
1.83-1.85	0.218	211	0.1637	3940	X-RAY DIFFRACTION	99.9
1.85-1.88	0.1923	181	0.1558	4017	X-RAY DIFFRACTION	99.93
1.88-1.91	0.2095	192	0.1503	3975	X-RAY DIFFRACTION	99.81
1.91-1.94	0.1622	187	0.1499	4003	X-RAY DIFFRACTION	99.88
1.94-1.97	0.1762	212	0.1522	3954	X-RAY DIFFRACTION	99.88
1.97-2.01	0.2091	197	0.1452	3967	X-RAY DIFFRACTION	99.86
2.01-2.05	0.1921	209	0.1462	3999	X-RAY DIFFRACTION	99.93
2.05-2.09	0.1775	187	0.1436	3987	X-RAY DIFFRACTION	99.9
2.09-2.13	0.1778	180	0.1441	4000	X-RAY DIFFRACTION	99.86
2.13-2.18	0.1732	217	0.1465	3955	X-RAY DIFFRACTION	99.93
2.18-2.24	0.1938	225	0.1375	3947	X-RAY DIFFRACTION	99.95
2.24-2.3	0.156	218	0.1321	3985	X-RAY DIFFRACTION	99.88
2.3-2.37	0.1696	218	0.1405	3980	X-RAY DIFFRACTION	99.86
2.37-2.44	0.1816	198	0.1426	3983	X-RAY DIFFRACTION	99.88
2.44-2.53	0.1747	220	0.1382	4014	X-RAY DIFFRACTION	100
2.53-2.63	0.1749	217	0.1452	3966	X-RAY DIFFRACTION	99.93
2.63-2.75	0.1685	211	0.1456	4019	X-RAY DIFFRACTION	99.93
2.75-2.9	0.1815	191	0.1505	4030	X-RAY DIFFRACTION	99.91
2.9-3.08	0.1833	242	0.1556	3955	X-RAY DIFFRACTION	99.88
3.08-3.32	0.1821	206	0.1536	4037	X-RAY DIFFRACTION	99.98
3.32-3.65	0.1504	257	0.1432	3985	X-RAY DIFFRACTION	99.98
3.65-4.18	0.1561	187	0.1247	4114	X-RAY DIFFRACTION	99.98
4.18-5.26	0.1325	242	0.117	4056	X-RAY DIFFRACTION	99.91
5.26-48.04	0.1729	237	0.1452	4209	X-RAY DIFFRACTION	99.87

Refinement TLS params.

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

ID	L11 (°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)
1	0.388695687092	-0.182461399651	0.000773655598555	0.597854566353	0.00116444276308	0.410690162271	0.00892585134706	-0.00678039496143	-0.0439587963476	0.0181648148368	-0.0149078507409	0.0634636546827	-0.00559416750949	-0.0183412574028	0.00914742399597	0.102095670452	-0.00601296124774	0.000591951933016	0.0938657981572	-0.00462942719747	0.102661149808	-14.7180788433	54.5309251873	32.9055245233
2	0.358433340532	0.0300262707226	-1.21664661071	0.112519208949	-0.48528466916	5.38942319648	0.0484828424383	0.0364106575657	0.046941082412	0.0258416597253	0.0198101456456	0.0115187030681	-0.148042942953	-0.18093630856	-0.0667299628325	0.0931172777822	-0.0347632350487	-0.00304399921791	0.0919006781626	-0.00705081572402	0.115206606694	-20.3353647988	60.1203167595	9.29001406807
3	1.2978575514	-0.183837694669	0.41964886257	0.941877072583	-0.142561377877	0.810413799435	0.0360352108223	0.0726005569242	-0.0254431903414	-0.0524906215462	-0.0115440398664	-0.00590748512008	0.0596846213049	0.0401612487807	-0.0250704169127	0.113497088556	-0.00368002422285	0.00456072797691	0.10411526356	-0.00325587437889	0.0652818688596	-10.1211117378	55.153817317	-3.01965076649
4	0.0961309732843	-0.0608268058878	0.0532790482325	0.452405666639	-0.149072660452	0.0895656261653	0.0229254986862	0.0514196171571	-0.0440084641414	-0.0866366570944	-0.0245820782202	-0.0150436242624	0.0358671780315	0.00789567707265	0.00370724921129	0.125192808062	-0.000669851795442	0.00340917325759	0.124611000504	-0.0153982386317	0.119872638284	-5.44450555869	35.9116213175	10.2528631949
5	5.37387792688	1.87196017192	-2.01899353857	2.69587998044	-0.692270118821	1.66596257643	-0.0638774956165	-0.053725710917	-0.290787421286	0.0427745455207	-0.0100378617486	-0.37267917887	0.0455280249366	0.0995487981265	0.0836179860771	0.125210970237	0.0163426546212	-0.0129323313185	0.0934410036132	-0.00702125309264	0.114543048373	10.1092326458	29.5947399021	23.6126971851
6	1.08437676454	0.197596847977	-0.000270861430718	1.79907157805	-0.288759820245	1.36235144617	0.0532750077196	0.178078490735	0.136526338042	-0.163772496578	-0.0273618816397	-0.0669807847337	-0.0931388942278	0.0539938457044	-0.00928233100562	0.136197423518	0.00609350230601	0.0175045250434	0.109290157966	-0.000722036032183	0.112069231111	-0.013700451669	28.9296423607	12.5300011857
7	0.536631766516	0.137312760728	0.0455573893959	0.389927705108	0.132323189684	0.29439200862	2.40153507723E-5	0.0154330379505	-0.00653636637969	-0.0682372121532	-0.00418904152282	-0.027343845368	-0.0223399896835	0.0142748197501	0.00451508715322	0.121959270249	0.0029544994751	0.00097157198901	0.103492380362	0.00303885200767	0.096845693854	3.87987335123	81.2496795591	16.4178669841
8	5.7055631324	0.36546168907	-0.587691861003	0.220764718948	0.0526161309001	0.156572808354	-0.0487902435921	0.226120728768	-0.154749772065	-0.0641910584269	0.0115638238576	-0.0163348734299	0.027161452451	-0.0168331610734	0.0285977341364	0.124980338006	0.00847434390483	-0.00734750537079	0.0910141147036	0.027827761979	0.071991116913	-18.6901634571	75.893948528	8.21731334878
9	0.161614221004	0.168309707762	0.0302871859921	0.390121096898	0.0832018181553	0.148247529437	0.00350588681051	-0.00853915155342	0.0134061481784	-0.0161804154977	-0.0333889292862	0.076629429734	-0.015533579967	-0.0513394612479	0.0342740276537	0.130703620217	0.0101544819564	-0.0125209976151	0.139484958651	-0.0096565213672	0.140837149757	-25.8864459675	90.4933609987	20.0013019976
10	1.45339234827	0.0201465448251	-0.376020633141	1.62929309392	-0.602824649094	1.66865260539	-0.0315640778991	-0.0335038458583	-0.039507957162	0.0755171283058	0.032871433482	0.109557830195	0.0598773256918	-0.148975083475	0.00272166940666	0.0990562145384	-0.000284097531805	-0.00232212578847	0.0780894382258	-0.0194308669375	0.104109375666	-14.2192719122	106.990734039	33.4405316028

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 166 )	A	A	2 - 166	1 - 165
2	2	chain 'A' and (resid 167 through 219 )	A	A	167 - 219	166 - 218
3	3	chain 'A' and (resid 220 through 337 )	A	A	220 - 337	219 - 336
4	4	chain 'A' and (resid 338 through 467 )	A	A	338 - 467	337 - 466
5	5	chain 'A' and (resid 468 through 501 )	A	A	468 - 501	467 - 500
6	6	chain 'A' and (resid 502 through 550 )	A	A	502 - 550	501 - 549
7	7	chain 'B' and (resid 2 through 166 )	B	I	2 - 166	1 - 165
8	8	chain 'B' and (resid 167 through 219 )	B	I	167 - 219	166 - 218
9	9	chain 'B' and (resid 220 through 467 )	B	I	220 - 467	219 - 466
10	10	chain 'B' and (resid 468 through 549 )	B	I	468 - 549	467 - 548

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