PDB-8bci: Crystal structure of short-chain dehydrogenase PA3128 from Pseudo...

ID or keywords:

Entry

Database: PDB / ID: 8bci

Title

Crystal structure of short-chain dehydrogenase PA3128 from Pseudomonas aeruginosa PAO1

Components

Probable short-chain dehydrogenase

Keywords

UNKNOWN FUNCTION / PA3128 / P. aeruginosa / SDR

Function / homology

Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Probable short-chain dehydrogenase

Function and homology information

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 Å

Authors

Popp, M.A. / Vit, A. / Blankenfeldt, W.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: The structure of short-chain dehydrogenase PA3128 from Pseudomonas aeruginosa PAO1
Authors: Popp, M.A. / Vit, A. / Blankenfeldt, W.

History

Deposition	Oct 16, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 30, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bci.cif.gz	535.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8bci.ent.gz	451.5 KB	Display	PDB format
PDBx/mmJSON format	8bci.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bci_validation.pdf.gz	475.3 KB	Display	wwPDB validaton report
Full document	8bci_full_validation.pdf.gz	482.9 KB	Display
Data in XML	8bci_validation.xml.gz	43.1 KB	Display
Data in CIF	8bci_validation.cif.gz	62.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bc/8bci ftp://data.pdbj.org/pub/pdb/validation_reports/bc/8bci	HTTPS FTP

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Related structure data

Related structure data	8bcjC 4iqgS S: Starting model for refinement 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

Deposited unit

A: Probable short-chain dehydrogenase

B: Probable short-chain dehydrogenase

C: Probable short-chain dehydrogenase

D: Probable short-chain dehydrogenase

hetero molecules

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

1

A: Probable short-chain dehydrogenase

B: Probable short-chain dehydrogenase

hetero molecules

defined by author
Evidence: gel filtration
53.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Probable short-chain dehydrogenase

D: Probable short-chain dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	221.335, 65.688, 66.269
Angle α, β, γ (deg.)	90.000, 107.350, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Probable short-chain dehydrogenase Mass: 26447.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA3128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZ96
#2: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 707 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.17 Å³/Da / Density % sol: 43.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 1 M LiCl, 12 % PEG 6000, 0.1 M MES pH 6.2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.918409 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.918409 Å / Relative weight: 1

Reflection

Resolution: 1.7→48.23 Å / Num. obs: 99754 / % possible obs: 99.9 % / Redundancy: 4.5 % / B_iso Wilson estimate: 19.12 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.068 / R_pim(I) all: 0.036 / R_rim(I) all: 0.077 / Net I/σ(I): 16.4 / Num. measured all: 449835 / Scaling rejects: 39

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.7-1.73	4.6	0.782	22560	4923	0.725	0.406	0.884	2.1	99.8
9.31-48.23	4.4	0.018	2860	645	1	0.009	0.02	87.1	98.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
XDS		data reduction
Aimless	0.1.29	data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IQG

4iqg

Resolution: 1.7→48.23 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1865	4965	4.98 %
R_work	0.1527	94769	-
obs	0.1544	99734	99.85 %

Solvent computation

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

Displacement parameters

B_iso max: 146.1 Å² / B_iso mean: 27.7143 Å² / B_iso min: 8.1 Å²

Refinement step

Cycle: final / Resolution: 1.7→48.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6980	0	164	707	7851
B_iso mean	-	-	43.85	35.11	-
Num. residues	-	-	-	-	952

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.72	0.3018	176	0.2639	3106	3282	100
1.72-1.74	0.2739	149	0.2439	3147	3296	100
1.74-1.76	0.2831	165	0.2302	3146	3311	100
1.76-1.78	0.269	170	0.2179	3135	3305	100
1.78-1.81	0.2881	147	0.2134	3161	3308	100
1.81-1.83	0.2125	170	0.1976	3164	3334	100
1.83-1.86	0.2276	155	0.1817	3130	3285	100
1.86-1.89	0.2542	170	0.1775	3132	3302	100
1.89-1.91	0.2153	162	0.1723	3109	3271	100
1.91-1.95	0.2021	184	0.1639	3151	3335	100
1.95-1.98	0.1992	178	0.1702	3146	3324	100
1.98-2.02	0.2181	173	0.1697	3127	3300	100
2.02-2.05	0.2111	153	0.1706	3175	3328	100
2.05-2.1	0.2196	159	0.1709	3138	3297	100
2.1-2.14	0.1835	141	0.141	3186	3327	100
2.14-2.19	0.1748	164	0.1344	3156	3320	100
2.19-2.25	0.1742	163	0.1353	3144	3307	100
2.25-2.31	0.1908	163	0.1342	3167	3330	100
2.31-2.38	0.1744	163	0.1349	3144	3307	100
2.38-2.45	0.163	157	0.1394	3191	3348	100
2.45-2.54	0.1692	172	0.1337	3144	3316	100
2.54-2.64	0.1374	170	0.1368	3174	3344	100
2.64-2.76	0.1865	163	0.1441	3181	3344	100
2.76-2.91	0.1635	154	0.1447	3169	3323	100
2.91-3.09	0.1767	183	0.1414	3150	3333	100
3.09-3.33	0.1872	160	0.1476	3166	3326	100
3.33-3.66	0.1764	169	0.1333	3187	3356	100
3.66-4.19	0.1835	166	0.1333	3169	3335	100
4.19-5.28	0.1531	164	0.1273	3228	3392	100
5.28-48.23	0.1858	202	0.1948	3246	3448	99

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	0.0297	0.0065	0.0307	0.0075	0.0117	0.0222	0.0136	-0.0062	0.036	0.0063	-0.002	-0.007	-0.1257	0.2138	0.0062	0.148	-0.0552	0.0255	0.1883	-0.0228	0.1241	251.6054	46.68	79.1024
2	0.0267	-0.0167	-0.0316	0.087	0.0504	0.0724	0.0149	0.0629	0.0103	0.0959	0.0044	-0.0189	0.0062	0.2016	-0.0023	0.1397	-0.1148	-0.0013	0.2866	0.0089	0.1459	257.8445	46.5045	84.3327
3	0.1215	0.0452	0.0302	0.0262	-0.0199	0.219	0.0879	0.0041	-0.036	0.0818	-0.0979	-0.022	-0.0784	0.1034	-0.0693	0.1623	-0.0124	0.0177	0.1288	-0.031	0.1249	242.5106	37.3122	85.558
4	0.0085	0.0073	-0.0254	0.0101	-0.0074	0.0193	0.0322	-0.0048	-0.0007	-0.073	-0.0492	-0.002	0.0065	0.1122	-0.01	0.1428	0.0325	0.0235	0.1377	-0.0323	0.1199	242.9142	28.9493	72.3148
5	0.038	0.022	-0.02	0.029	-0.049	0.0992	0.0773	0.0156	0.0089	-0.0214	-0.0835	-0.0014	0.0068	0.0828	-0.0209	0.1088	0.0284	0.0227	0.1158	-0.0253	0.1248	241.4418	33.0675	74.6295
6	0.069	0.0019	0.0027	0.0531	-0.0152	0.0478	0.0176	0.0322	-0.0275	-0.0388	0.0054	0.0563	-0.0155	0.1726	0.0202	0.1274	0.0233	0.0359	0.1765	-0.035	0.1003	246.9079	36.1189	65.3437
7	0.0166	0.0017	-0.0019	0.0134	-0.0131	0.0112	0.035	-0.0418	-0.1245	-0.0759	0.1174	0.0969	0.2028	-0.1349	0.0111	0.216	-0.0104	-0.0363	0.1188	0.0011	0.217	222.2841	3.8954	83.1059
8	0.0179	-0.0207	-0.0173	0.0227	0.0084	0.0399	-0.0362	-0.1311	-0.0741	0.0854	0.0943	0.0369	0.2763	-0.042	0.0015	0.247	-0.0229	-0.0052	0.1592	0.0588	0.2158	226.8761	2.312	90.8141
9	0.0583	0.0037	0.0024	0.0135	-0.0076	0.0561	0.08	-0.1113	-0.0346	0.0894	-0.0502	0.1319	0.0728	0.0475	0.0646	0.163	0.002	0.0365	0.0867	-0.0232	0.1332	230.4026	23.6725	87.0489
10	0.0079	-0.0161	0.0012	0.0217	-0.0003	-0.0001	0.0418	-0.0947	-0.0711	-0.0284	-0.0034	-0.015	0.0668	0.1096	0.0036	0.174	0.0811	-0.0207	0.1233	-0.0188	0.1609	240.1932	5.1334	79.2391
11	0.0158	0.0262	-0.0161	0.0345	-0.0213	0.0419	0.0564	0.0238	-0.0285	-0.0309	-0.0648	0.1171	0.0574	0.0332	0.0179	0.111	0.0283	-0.0007	0.0854	-0.0299	0.1396	231.4059	21.3932	75.9504
12	0.026	-0.0053	0.0138	0.0199	-0.0204	0.0383	0.0278	-0.0442	0.0607	-0.0557	-0.0018	0.0372	0.0782	-0.025	0.0034	0.1288	0.0247	-0.0307	0.1259	-0.0362	0.234	218.0263	21.6767	74.5022
13	0.0201	0.005	0.0167	0.0099	-0.0122	0.0214	0.0472	-0.0255	0.0443	-0.129	0.0137	0.0956	0.1217	-0.0093	0.0074	0.1703	0.0184	-0.0528	0.1244	-0.0309	0.207	222.8232	12.3256	69.3839
14	0.0093	0.0012	0.0084	0.016	0.0098	0.0132	0.0963	0.0161	-0.1093	-0.0683	0.0489	0.0275	0.137	0.0156	0.0314	0.2452	0.0025	-0.1097	0.2084	-0.0745	0.2718	214.8894	7.1922	48.3643
15	0.0117	0.0172	0.0157	0.0116	0.0059	0.0166	0.023	0.1418	-0.1369	-0.0585	-0.037	0.0589	0.2176	-0.1164	-0.0625	0.2408	-0.039	-0.3537	0.2214	-0.1816	0.2505	209.5321	9.8723	41.5774
16	0.0428	0.0274	0.0016	0.2629	0.0297	0.1832	0.0461	0.1355	-0.0955	-0.1675	0.0449	0.1144	0.0811	0.0196	0.1189	0.1628	0.026	-0.0499	0.2277	-0.0472	0.1953	218.8681	22.5451	46.4332
17	0.024	0.0121	0.0116	0.0506	0.0004	0.0158	0.0659	0.0241	-0.06	-0.0832	0.0005	0.074	0.0398	0.0233	0.0031	0.1244	0.028	-0.0177	0.1615	-0.0317	0.1631	225.2892	23.4003	53.7855
18	0.0281	-0.0051	-0.0004	0.049	-0.0407	0.0835	0.1064	0.0338	0.0077	-0.1058	-0.0094	0.0367	0.1257	-0.0169	0.0374	0.1598	0.0417	-0.045	0.1345	-0.0461	0.1957	225.1775	12.4379	60.0488
19	0.0016	-0.0046	-0.0013	0.0143	-0.0035	0.011	0.0157	0.0493	0.0133	-0.0975	0.0654	0.0879	-0.1646	0.0097	0	0.2638	-0.0076	0.0267	0.2144	0.0316	0.1447	237.4095	52.2703	46.9536
20	0.0076	0.0013	-0.0049	0.0195	0.013	0.0052	0.0131	0.1776	0.1395	0.0438	-0.0365	-0.0045	-0.1742	-0.0221	-0.0041	0.4571	-0.0203	-0.0398	0.2197	0.0834	0.222	234.95	56.6278	40.9883
21	0.0031	0.0005	0.0029	0.0008	-0.0048	0.0035	0.0274	0.0495	-0.0251	-0.0583	-0.0264	-0.0025	-0.0409	0.0052	0.0013	0.3225	-0.0313	0.0563	0.3457	0.0269	0.1307	239.4447	45.4167	33.7411
22	0.0704	0.0431	-0.0002	0.4853	-0.0367	0.0454	0.032	0.1708	0.0419	-0.2849	0.0695	0.2116	-0.0775	0.1194	0.0602	0.1764	0.0146	0.0052	0.2892	0.0011	0.1095	231.1634	37.4208	44.2258
23	0.0043	0.005	0.0036	0.0138	0.0003	0.0019	0.0583	0.0047	0.0261	-0.0536	-0.0036	0.0839	-0.0491	0.0525	0	0.1356	0.0302	0.0164	0.1807	-0.0146	0.1537	225.7695	37.3231	56.2149
24	0.029	0.045	0.0069	0.0488	-0.0378	0.0813	0.0164	0.0453	0.0359	-0.0693	0.0296	0.0573	-0.0724	0.0419	0.053	0.1162	0.0327	0.0306	0.1652	-0.029	0.1411	232.2839	37.591	56.2432
25	0.0095	0.0101	-0.006	0.0058	0.0122	0.0244	0.0577	0.0323	0.033	-0.0651	-0.0173	0.0731	-0.0768	0.1106	0	0.1659	0.0113	0.0399	0.1638	-0.0209	0.1387	238.7142	43.2733	60.1146

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 36 )	A	0 - 36
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 63 )	A	37 - 63
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 135 )	A	64 - 135
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 136 through 154 )	A	136 - 154
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 155 through 200 )	A	155 - 200
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 201 through 248 )	A	201 - 248
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 36 )	B	0 - 36
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 37 through 78 )	B	37 - 78
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 79 through 113 )	B	79 - 113
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 114 through 135 )	B	114 - 135
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 136 through 178 )	B	136 - 178
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 179 through 218 )	B	179 - 218
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 219 through 248 )	B	219 - 248
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 2 through 36 )	C	2 - 36
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 37 through 78 )	C	37 - 78
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 79 through 135 )	C	79 - 135
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 136 through 178 )	C	136 - 178
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 179 through 248 )	C	179 - 248
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1 through 36 )	D	1 - 36
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 37 through 63 )	D	37 - 63
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 64 through 78 )	D	64 - 78
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 79 through 135 )	D	79 - 135
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 136 through 154 )	D	136 - 154
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 155 through 218 )	D	155 - 218
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 219 through 248 )	D	219 - 248

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