PDB-9myr: Sal-Shy(DUF35) aldolase from Comamonas testosteroni

ID or keywords:

Entry

Database: PDB / ID: 9myr

Title

Sal-Shy(DUF35) aldolase from Comamonas testosteroni

Components

Acyl dehydratase
Nonspecific lipid-transfer protein

Keywords

LIPID TRANSPORT / Complex / Aldolase / Steroids / Cleavage / DUF35 / Sal / Shy

Function / homology

Function and homology information

acetyl-CoA C-acyltransferase activity
Similarity search - Function

Biological species

Comamonas testosteroni KF-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Rolfe, N. / Schroeter, K.L. / Forrester, T.J.B. / Kimber, M.S. / Seah, S.Y.K.

Funding support

Canada, 2items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: Sal is a proteobacterial bile acid aldolase that repurposes key thiolase catalytic residues for retroaldol cleavage of C 5 steroid side chains.
Authors: Rolfe, N. / Schroeter, K.L. / Forrester, T.J. / Kimber, M.S. / Seah, S.Y.

History

Deposition	Jan 22, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9myr.cif.gz	735 KB	Display	PDBx/mmCIF format
PDB format	pdb9myr.ent.gz	508.6 KB	Display	PDB format
PDBx/mmJSON format	9myr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9myr_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9myr_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9myr_validation.xml.gz	58.3 KB	Display
Data in CIF	9myr_validation.cif.gz	79.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/my/9myr ftp://data.pdbj.org/pub/pdb/validation_reports/my/9myr	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#216 - Dec 2017 Biodegradable Plastic similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2)

Deposited unit

A: Nonspecific lipid-transfer protein

B: Acyl dehydratase

C: Nonspecific lipid-transfer protein

D: Acyl dehydratase

hetero molecules

124 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	85.460, 104.420, 112.850
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
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

#1: Protein	Nonspecific lipid-transfer protein Mass: 46012.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Strain: DSM 14576 / KF-1 / Gene: CtesDRAFT_PD3654 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7X4S8
#2: Protein	Acyl dehydratase Mass: 16060.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Strain: DSM 14576 / KF-1 / Gene: CtesDRAFT_PD3653 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7X4S7
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1031 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.35 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium citrate tribasic monohydrate, 20% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.52127 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.52127 Å / Relative weight: 1
Reflection	Resolution: 1.95→47.09 Å / Num. obs: 72083 / % possible obs: 97.2 % / Redundancy: 6.44 % / B_iso Wilson estimate: 23.26 Å² / CC_1/2: 0.997 / Net I/σ(I): 9.65
Reflection shell	Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 7033 / CC_1/2: 0.503

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→47.09 Å / SU ML: 0.2359 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.8832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2311	3333	5 %
R_work	0.1826	63342	-
obs	0.1851	66675	89.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 27.57 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→47.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8120	0	2	1031	9153

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0023	8341
X-RAY DIFFRACTION	f_angle_d	0.5598	11309
X-RAY DIFFRACTION	f_chiral_restr	0.0424	1235
X-RAY DIFFRACTION	f_plane_restr	0.0048	1499
X-RAY DIFFRACTION	f_dihedral_angle_d	15.1765	3049

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 (%)
1.95-1.98	0.3811	110	0.2981	2095	X-RAY DIFFRACTION	72.11
1.98-2.01	0.3002	110	0.2932	2192	X-RAY DIFFRACTION	75.85
2.01-2.04	0.3477	119	0.2745	2286	X-RAY DIFFRACTION	79.22
2.04-2.07	0.3366	122	0.2554	2331	X-RAY DIFFRACTION	79.85
2.07-2.11	0.3133	127	0.2439	2430	X-RAY DIFFRACTION	83.45
2.11-2.15	0.3124	132	0.2331	2410	X-RAY DIFFRACTION	83.56
2.15-2.19	0.313	127	0.2234	2458	X-RAY DIFFRACTION	84.5
2.19-2.23	0.2777	134	0.2174	2526	X-RAY DIFFRACTION	86.53
2.23-2.28	0.2765	138	0.2121	2567	X-RAY DIFFRACTION	88.83
2.28-2.33	0.2706	140	0.2162	2571	X-RAY DIFFRACTION	88.65
2.33-2.39	0.2586	135	0.2013	2602	X-RAY DIFFRACTION	89.01
2.39-2.46	0.2778	136	0.2015	2666	X-RAY DIFFRACTION	91.12
2.46-2.53	0.2631	139	0.1951	2659	X-RAY DIFFRACTION	91.14
2.53-2.61	0.2349	145	0.1957	2718	X-RAY DIFFRACTION	93.14
2.61-2.7	0.2708	148	0.1951	2778	X-RAY DIFFRACTION	94.48
2.7-2.81	0.2368	142	0.202	2766	X-RAY DIFFRACTION	94.91
2.81-2.94	0.2751	149	0.1951	2804	X-RAY DIFFRACTION	95.44
2.94-3.1	0.2505	149	0.1869	2817	X-RAY DIFFRACTION	96.17
3.1-3.29	0.2437	151	0.1809	2881	X-RAY DIFFRACTION	96.81
3.29-3.54	0.2092	151	0.1659	2871	X-RAY DIFFRACTION	97.23
3.54-3.9	0.1821	151	0.1448	2893	X-RAY DIFFRACTION	97.5
3.9-4.46	0.1703	156	0.1275	2925	X-RAY DIFFRACTION	97.97
4.46-5.62	0.1713	157	0.1322	2983	X-RAY DIFFRACTION	98.65
5.62-47.09	0.1921	165	0.1806	3113	X-RAY DIFFRACTION	98.76

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	1.91451392121	-0.286557018986	0.203545254447	1.96448074174	-0.226253123224	2.66627857908	0.0346289948951	-0.108502283004	0.0802592315608	0.0725883829895	-0.0101303705409	-0.0709765920446	-0.177593735055	-0.00558420611061	-0.0285313631633	0.126301636949	-0.00221845510254	0.00957083391798	0.0887821017575	-0.00278332414627	0.100430411122	61.6523460058	81.4840383285	24.8927439856
2	0.187832789937	0.3011457447	-0.426479125851	1.99114971401	-0.630654247036	0.959868157918	0.0152007819829	0.0645789001435	0.056647176641	0.0144388308624	0.0522753695663	0.0479065349752	-0.0682720294004	-0.0258084477748	-0.0811225772106	0.141133137403	0.0245707241961	0.00742382209372	0.149157742077	-0.0169222115234	0.123675512817	56.0807421235	75.2314407814	27.5441898281
3	1.01630498715	0.399680366321	0.506152394365	2.03849450532	1.08526478342	2.30949598136	-0.0342509638439	-0.0878430129927	0.0260014668408	0.268494721446	-0.070219493692	0.224988124791	-0.0923464196836	-0.2773343334	0.035162021149	0.200857855859	0.0220236636418	0.0198378227011	0.123679592519	0.0259298165162	0.140381128894	38.591683277	67.9419757468	44.1776665091
4	0.900198521359	0.0281405683296	-0.25499733392	1.01496718461	-0.352820523437	1.10097713255	-0.0333567053597	-0.153211779252	0.106765623389	0.222392169932	0.0799060344005	-0.0292679081903	-0.175965709703	0.114347535086	-0.0399355046157	0.225973641683	0.0215966686181	-0.0304000184882	0.180047789994	-0.0299147613742	0.133205527025	54.4324969372	83.3278225583	46.0611476147
5	3.67300074472	1.83517096337	-0.213225994872	5.66646250259	-1.4581574055	9.43358413324	-0.0343276827131	0.556299739655	0.478247735207	-0.0333423506079	0.0469288321639	1.34833800099	-0.743617280614	-0.562358393402	0.0531270913996	0.216608143445	-0.0460962488987	-0.0429193040454	0.241567524901	-0.0153602405343	0.412401527181	31.0880316849	56.6153794579	29.6342831187
6	1.70929379908	-0.353518014918	-0.343700219677	1.88524474067	0.478865349488	2.21220004132	0.0228720143345	-0.0278568713132	0.10133676571	0.0352633766708	-0.0884091351307	0.210703559231	-0.0692435709486	-0.301678149012	0.0811238246689	0.196527632243	-0.00628926732839	0.00601390724172	0.144324075758	-0.0210607503713	0.154551623851	35.7547404705	55.2392385139	42.7263666574
7	3.83761877827	0.719537974375	-1.10262388591	4.77923283258	1.47527418966	3.94686281875	-0.0314660533037	0.0449148823075	0.0535707502041	0.199117036899	-0.124209828921	0.498797014751	0.0818175882613	-0.681615064042	0.16873499311	0.166493466011	0.0271536859853	0.0592928573765	0.230461392055	-0.0309066213906	0.308460851823	23.8302510392	56.0356916162	44.3906854194
8	2.33192156319	0.0756640898882	-0.222433139263	1.34749416513	0.1401023266	1.53233091686	-0.103079646669	0.04015225645	-0.11570656585	0.0827845592969	0.0056391637768	-0.100357417446	0.0333980286254	0.0262392352524	0.0870038534754	0.128450959124	-0.00111349672223	0.00496098443003	0.0952485265867	0.00283488425435	0.100052532527	58.3260070895	53.7008559707	29.8680795545
9	0.831268234614	0.0661175485851	-0.685942425315	1.61209678553	0.0186554314396	0.687011262439	-0.0433136288217	-0.00158430725669	-0.0378036308678	-0.0347868981661	-0.0181425932451	-0.0548090043401	0.0213689568055	-0.0261460273658	0.0523931919298	0.141951027278	0.0123122609847	-0.00386929639343	0.121750246056	-0.0325773930411	0.112746534894	59.0338870282	61.4920314059	26.2035020143
10	2.26138582908	-1.14478980489	-1.02721041292	1.14261354152	0.355670545668	0.844004877181	0.0452399669201	0.107097974799	-0.0106279376607	-0.0509621720782	-0.0465937029176	0.0212157535567	-0.190434320039	-0.0300751199309	0.0153237281627	0.213708148075	0.00284103057668	0.0133055668707	0.184359464481	-0.0259462903526	0.146056024574	66.8114130225	68.1043465309	1.37142838436
11	0.826675537764	-0.138410788154	-0.271534689055	0.63564412795	-0.111343332177	1.38636522329	-0.0553338530298	-0.0476302317919	-0.137938883149	-0.0479557376942	-0.0591202736207	-0.152682612297	0.134602699134	0.224382865794	0.102062549439	0.136392784766	0.0288394767919	0.0105296720946	0.178476606617	0.0171840440321	0.19919598006	74.9529803778	53.1842746331	15.5278861331
12	5.2928812832	-0.833479379634	-1.81334459617	7.07195879487	0.603005982597	6.0262657909	-0.0241849434257	0.257527131004	-0.0766408629317	-0.477911460733	-0.276173814971	0.618763993645	0.218077306622	-0.429783156254	0.402468767585	0.232959812941	0.0687988333193	-0.0380270167615	0.223430177185	-0.00342596444781	0.145563026979	50.2456470181	79.4673815748	1.04607298156
13	0.84602860055	-0.310348281733	-0.0433883209624	2.16097263496	1.32263850397	1.65427047675	0.15068881472	0.151098882596	0.0365809934107	-0.179419588001	-0.0960333743911	-0.00808810838074	-0.173196405117	0.0459041815916	-0.0314161262296	0.230950319584	0.0257821075317	0.0376368294271	0.20158993469	0.0291103533877	0.16846628596	63.8703840969	81.5973564277	-0.0515835232534
14	4.41434670042	-1.26592800163	1.51334428179	2.35165918532	-0.374848613378	1.81451752136	0.171936116328	0.480783196772	0.000317499878937	-0.448326310293	-0.150771716309	0.0433108546074	-0.251580273152	-0.143836182211	0.0194779526753	0.372484795241	0.036740305668	0.0152737572814	0.305044209104	-0.0103046680225	0.117938494446	61.8928072508	78.0249423194	-12.8407424001

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 1 through 87 )	A	A	1 - 87	1 - 87
2	2	chain 'A' and (resid 88 through 145 )	A	A	88 - 145	88 - 136
3	3	chain 'A' and (resid 146 through 179 )	A	A	146 - 179	137 - 170
4	4	chain 'A' and (resid 180 through 404 )	A	A	180 - 404	171 - 395
5	5	chain 'B' and (resid 3 through 14 )	B	B	3 - 14	1 - 12
6	6	chain 'B' and (resid 15 through 107 )	B	B	15 - 107	13 - 105
7	7	chain 'B' and (resid 108 through 144 )	B	B	108 - 144	106 - 142
8	8	chain 'C' and (resid 1 through 75 )	C	C	1 - 75	1 - 75
9	9	chain 'C' and (resid 76 through 145 )	C	C	76 - 145	76 - 136
10	10	chain 'C' and (resid 146 through 179 )	C	C	146 - 179	137 - 170
11	11	chain 'C' and (resid 180 through 404 )	C	C	180 - 404	171 - 395
12	12	chain 'D' and (resid 3 through 14 )	D	D	3 - 14	1 - 12
13	13	chain 'D' and (resid 15 through 99 )	D	D	15 - 99	13 - 97
14	14	chain 'D' and (resid 100 through 144 )	D	D	100 - 144	98 - 142

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