PDB-9nzb: Crystal Structure of acyl-CoA lyase subunit beta from Pseudomonas...

ID or keywords:

Entry

Database: PDB / ID: 9nzb

Title

Crystal Structure of acyl-CoA lyase subunit beta from Pseudomonas aeruginosa PAO1

Components

Acyl-CoA lyase beta chain

Keywords

LYASE / Center for Structural Biology of Infectious Diseases / CSBID / acyl-CoA lyase / Structural Genomics

Function / homology

Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / oxaloacetate metabolic process / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / lyase activity / magnesium ion binding / Probable acyl-CoA lyase beta chain

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Minasov, G. / Shukla, S. / Shuvalova, L. / Brunzelle, J.S. / Warwzak, Z. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of acyl-CoA lyase subunit beta from Pseudomonas aeruginosa PAO1
Authors: Minasov, G. / Shukla, S. / Shuvalova, L. / Brunzelle, J.S. / Warwzak, Z. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)

History

Deposition	Mar 31, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 9, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9nzb.cif.gz	616.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9nzb.ent.gz	512.8 KB	Display	PDB format
PDBx/mmJSON format	9nzb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/9nzb ftp://data.pdbj.org/pub/pdb/validation_reports/nz/9nzb	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
Other databases	TargetTrack: CSBID-IDP98636

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (2)

Deposited unit

A: Acyl-CoA lyase beta chain

B: Acyl-CoA lyase beta chain

C: Acyl-CoA lyase beta chain

D: Acyl-CoA lyase beta chain

E: Acyl-CoA lyase beta chain

F: Acyl-CoA lyase beta chain

176 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Acyl-CoA lyase beta chain

B: Acyl-CoA lyase beta chain

C: Acyl-CoA lyase beta chain

defined by author&software
88 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Acyl-CoA lyase beta chain

E: Acyl-CoA lyase beta chain

F: Acyl-CoA lyase beta chain

defined by author&software
88 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.828, 198.038, 65.351
Angle α, β, γ (deg.)	90.00, 91.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Acyl-CoA lyase beta chain Mass: 29330.590 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA0883 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I562
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1303 / Source method: isolated from a natural source / Formula: H₂O
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: 2.23 Å³/Da / Density % sol: 45 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 18.0 mg/ml, 0.15M Sodium chloride, 0.01M Tris-HCl (pH 8.0); Screen: Classics II (G1), 0.2M Sodium chloride, 0.1M Tris (pH 8.5), 25% (w/v) PEG 3350; Cryo: Reservoir.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 20, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.85→30 Å / Num. obs: 134881 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / B_iso Wilson estimate: 24.5 Å² / CC_1/2: 0.992 / CC star: 0.998 / R_merge(I) obs: 0.077 / R_pim(I) all: 0.054 / R_rim(I) all: 0.095 / R_sym value: 0.077 / Χ²: 1.001 / Net I/σ(I): 12.6
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.703 / Mean I/σ(I) obs: 2 / Num. unique obs: 5212 / CC_1/2: 0.445 / R_pim(I) all: 0.517 / R_rim(I) all: 0.876 / R_sym value: 0.703 / Χ²: 0.995 / % possible all: 73.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→29.48 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.945 / SU B: 6.044 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20888	6719	5 %	RANDOM
R_work	0.17228	-	-	-
obs	0.17416	126517	95.37 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 31.819 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.73 Å²	0 Å²	1.07 Å²
2-	-	1.2 Å²	-0 Å²
3-	-	-	-0.52 Å²

Refinement step

Cycle: 1 / Resolution: 1.85→29.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11704	0	0	1303	13007

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	12202
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	12113
X-RAY DIFFRACTION	r_angle_refined_deg	1.587	1.837	16622
X-RAY DIFFRACTION	r_angle_other_deg	0.564	1.752	27701
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.265	5	1613
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	1.709	5	156
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	7.965	10	1979
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	1911
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	15159
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	2813
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.308	0.858	6392
X-RAY DIFFRACTION	r_mcbond_other	1.307	0.858	6391
X-RAY DIFFRACTION	r_mcangle_it	2.157	1.515	8025
X-RAY DIFFRACTION	r_mcangle_other	2.157	1.516	8026
X-RAY DIFFRACTION	r_scbond_it	2.082	1.173	5810
X-RAY DIFFRACTION	r_scbond_other	2.082	1.173	5811
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.374	2.018	8598
X-RAY DIFFRACTION	r_long_range_B_refined	8.393	12.73	14019
X-RAY DIFFRACTION	r_long_range_B_other	8.342	9.81	13671
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.256	345	-
R_work	0.242	8163	-
obs	-	-	82.67 %

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	1.4341	-0.6635	-0.2758	2.4802	0.2825	1.4042	-0.079	-0.0672	0.0634	-0.0093	0.0071	-0.138	0.0383	0.124	0.0719	0.2337	0.0013	-0.0723	0.1355	0.002	0.269	31.002	-2.673	31.732
2	0.9783	-0.3225	0.085	0.8755	-0.0716	0.8085	-0.0361	-0.0093	-0.0586	-0.033	0.0497	0.0465	0.0339	-0.0453	-0.0136	0.2605	-0.0196	-0.0751	0.1373	0.0056	0.285	15.917	-0.072	27.5
3	1.1339	-0.7141	-0.147	3.5032	0.3489	0.8919	0.0432	-0.0622	0.1776	0.1731	0.0776	-0.0837	-0.0988	-0.0251	-0.1208	0.2929	-0.008	-0.0376	0.1303	-0.0021	0.2912	21.831	18.75	32.036
4	7.2971	-3.8173	-3.7544	2.088	2.6037	14.2905	0.4556	-0.2911	0.0584	-0.0282	0.1045	-0.041	0.7069	-1.0681	-0.56	0.5592	-0.1003	0.0527	0.2631	0.0398	0.2796	14.034	22.054	45.611
5	1.9788	-1.0291	1.0236	1.6801	-0.5653	2.7809	0.0836	0.2029	0.1122	-0.1895	-0.0938	-0.0656	-0.0683	0.1383	0.0102	0.3091	-0.0115	-0.0611	0.1776	0.0124	0.2493	-5.679	0.657	-9.679
6	0.6845	0.0341	0.2153	0.8786	0.2415	1.4374	-0.0209	0.0548	0.0289	-0.0076	-0.0107	0.0175	-0.0364	0.0007	0.0316	0.2774	0.0014	-0.0636	0.156	0.0115	0.2501	-6.403	1.331	0.932
7	2.7211	0.4959	-1.7695	10.3559	-1.8193	12.5974	0.1212	-0.0436	0.0075	-0.1054	-0.577	-2.0658	-0.2806	-0.0109	0.4558	0.0141	-0.0074	0.02	0.3562	0.057	0.4425	23.313	-3.488	-3.292
8	5.607	-3.7324	5.6492	8.6062	-6.8669	9.199	0.2261	0.1329	-0.342	0.2716	-0.3445	-0.9149	0.4171	0.6837	0.1184	0.225	0.0292	-0.1246	0.2736	0.0124	0.3596	15.939	-6.016	1.233
9	1.088	-0.215	0.1292	1.565	-0.9333	3.317	-0.0846	-0.0236	0.2109	0.4433	0.1036	-0.0188	-0.6737	-0.2452	-0.019	0.4399	0.1058	-0.0633	0.1243	0.0064	0.3059	-16.049	29.716	35.686
10	1.5195	-0.0636	0.0467	1.1006	-0.2736	1.4688	-0.0434	-0.1563	0.0806	0.2088	0.1005	0.036	-0.2072	-0.1899	-0.057	0.3026	0.0575	-0.0636	0.168	0.0067	0.2693	-12.165	18.302	35.445
11	0.676	-0.8344	-0.3639	3.076	-0.1858	4.8784	0.0936	0.1538	0.1027	-0.2751	0.0571	-0.1608	-0.4035	-0.2715	-0.1507	0.3183	0.0131	-0.0229	0.1535	0.0391	0.3002	-13.21	29.824	17.066
12	4.7085	-0.655	-3.1484	11.1982	4.5392	3.6625	-0.0015	0.566	-0.5073	-0.2635	-0.4519	0.5242	-0.1825	-0.5281	0.4534	0.2674	0.0196	-0.0463	0.283	-0.0326	0.3286	-22.98	21.125	11.835
13	1.9472	-0.145	-1.0996	1.6691	-0.3746	4.1688	-0.0016	0.298	-0.3339	-0.2666	-0.1329	-0.0588	0.4961	-0.3817	0.1345	0.3187	-0.0197	0.0075	0.163	-0.0488	0.3212	-47.822	36.845	8.837
14	3.6411	0.6318	-1.5871	3.4612	0.7917	2.2805	-0.156	0.5392	-0.5056	-0.444	-0.1772	0.0751	0.2695	-0.4608	0.3332	0.3209	-0.0412	-0.0453	0.2814	-0.1101	0.3076	-53.117	39.521	4.052
15	1.4474	-0.0737	0.0066	0.825	0.0587	1.1262	0.0181	0.1016	-0.051	-0.0681	-0.0048	-0.0246	0.0441	-0.0862	-0.0133	0.2708	0.0001	-0.0134	0.1313	0.0029	0.2952	-41.963	49.39	15.135
16	1.0238	-0.1485	0.5189	1.6091	-0.8156	3.7435	-0.046	-0.1146	-0.0775	0.2242	0.1343	0.0038	0.1287	-0.3394	-0.0883	0.2997	0.0061	0.0072	0.1558	0.0231	0.3049	-47.018	37.141	30.683
17	5.5461	-1.4359	1.649	10.7383	4.7611	4.6703	-0.3957	-0.4327	0.4154	0.447	0.1629	0.5568	0.0372	-0.6263	0.2328	0.2809	0.0903	0.0452	0.2714	-0.0097	0.3074	-56.155	45.49	36.306
18	2.004	0.1523	-1.4876	1.9344	-0.3734	2.4133	0.0338	-0.3139	0.0091	0.1513	0.0474	0.04	0.0471	0.1379	-0.0812	0.3352	-0.0214	0.003	0.1684	-0.0103	0.2397	-44.856	67.31	57.601
19	1.1558	-0.3143	-0.734	0.6784	-0.0546	1.4334	-0.0194	-0.1549	-0.0275	0.0349	0.0125	-0.0232	0.0634	0.098	0.0069	0.3109	-0.0142	-0.0094	0.1566	-0.0032	0.2906	-37.652	63.543	44.028
20	2.6501	1.4636	1.0473	13.8224	-8.9765	7.4424	-0.085	-0.0852	-0.9424	0.1773	0.1309	-1.0446	-0.2084	-0.1158	-0.0459	0.0379	0.0123	0.1067	0.5291	-0.0539	0.6151	-10.29	69.441	52.43
21	4.0943	0.5179	-4.0238	11.3433	-7.1652	7.8843	-0.0736	-0.9671	0.5292	0.0518	0.0168	-0.9337	0.041	0.8715	0.0568	0.1001	-0.0266	0.0005	0.4242	-0.1321	0.4337	-18.054	70.806	48.457
22	2.4902	0.304	0.1577	2.5578	-0.2022	0.9069	-0.0791	-0.0443	0.0518	0.0336	-0.0079	-0.2639	-0.0464	0.0122	0.087	0.251	0.009	-0.0004	0.1358	-0.0013	0.3513	-0.87	69.617	17.34
23	1.4834	0.4784	-0.6929	0.8977	0.0503	0.8263	-0.051	0.0172	0.106	-0.0191	0.0541	0.0819	0.0349	0.0671	-0.0031	0.2637	0.0171	-0.0096	0.127	0.012	0.3457	-17.833	68.271	20.288
24	1.9916	0.9181	0.5067	4.2218	0.1523	1.2906	-0.0204	0.0322	-0.2147	-0.1735	0.1453	-0.2972	0.1123	0.0657	-0.1248	0.2563	0.0243	-0.0089	0.1258	-0.0055	0.3285	-9.437	48.942	18.243
25	6.4482	0.8746	6.4925	3.0503	5.6174	14.8054	0.334	-0.0714	-0.1125	-0.3263	-0.2056	-0.0967	-0.5252	-0.9625	-0.1285	0.4247	0.1505	-0.021	0.6315	-0.0171	0.2214	-17.281	47.309	4.783

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 72
2	X-RAY DIFFRACTION	2	A	73 - 196
3	X-RAY DIFFRACTION	3	A	197 - 240
4	X-RAY DIFFRACTION	4	A	241 - 275
5	X-RAY DIFFRACTION	5	B	1 - 40
6	X-RAY DIFFRACTION	6	B	41 - 227
7	X-RAY DIFFRACTION	7	B	228 - 240
8	X-RAY DIFFRACTION	8	B	257 - 273
9	X-RAY DIFFRACTION	9	C	1 - 42
10	X-RAY DIFFRACTION	10	C	43 - 190
11	X-RAY DIFFRACTION	11	C	191 - 242
12	X-RAY DIFFRACTION	12	C	256 - 274
13	X-RAY DIFFRACTION	13	D	1 - 50
14	X-RAY DIFFRACTION	14	D	51 - 71
15	X-RAY DIFFRACTION	15	D	72 - 196
16	X-RAY DIFFRACTION	16	D	197 - 242
17	X-RAY DIFFRACTION	17	D	254 - 274
18	X-RAY DIFFRACTION	18	E	3 - 71
19	X-RAY DIFFRACTION	19	E	72 - 227
20	X-RAY DIFFRACTION	20	E	228 - 241
21	X-RAY DIFFRACTION	21	E	260 - 273
22	X-RAY DIFFRACTION	22	F	2 - 73
23	X-RAY DIFFRACTION	23	F	74 - 182
24	X-RAY DIFFRACTION	24	F	183 - 242
25	X-RAY DIFFRACTION	25	F	257 - 274

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