PDB-3gem: Crystal structure of short-chain dehydrogenase from Pseudomonas s...

ID or keywords:

Entry

Database: PDB / ID: 3gem

Title

Crystal structure of short-chain dehydrogenase from Pseudomonas syringae

Components

Short chain dehydrogenase

Keywords

OXIDOREDUCTASE / structural genomics / APC65077 / Short-chain dehydrogenase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

dihydromonapterin reductase / dihydrofolate reductase / one-carbon metabolic process / oxidoreductase activity
Similarity search - Function

Biological species

Pseudomonas syringae pv. phaseolicola 1448A (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.83 Å

Authors

Osipiuk, J. / Xu, X. / Cui, H. / Nocek, B. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray crystal structure of short-chain dehydrogenase from Pseudomonas syringae.
Authors: Osipiuk, J. / Xu, X. / Cui, H. / Nocek, B. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.

History

Deposition	Feb 25, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3gem.cif.gz	201.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3gem.ent.gz	161.8 KB	Display	PDB format
PDBx/mmJSON format	3gem.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3gem_validation.pdf.gz	472.8 KB	Display	wwPDB validaton report
Full document	3gem_full_validation.pdf.gz	482 KB	Display
Data in XML	3gem_validation.xml.gz	47.4 KB	Display
Data in CIF	3gem_validation.cif.gz	64.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ge/3gem ftp://data.pdbj.org/pub/pdb/validation_reports/ge/3gem	HTTPS FTP

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Related structure data

Similar structure data	1lx6-1 3n74-d 1dfi-d 2eig-d 7krm-d 6xk0-d 4i5d-2 4oyr-d 4nim-3 1dfg-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC65077

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Short chain dehydrogenase

B: Short chain dehydrogenase

C: Short chain dehydrogenase

D: Short chain dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	74.198, 73.770, 162.168
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

AUTHORS STATE THAT THE TETRAMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE.

#1: Protein	Short chain dehydrogenase Mass: 28522.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola 1448A (bacteria) Strain: 1448A / Race 6 / Gene: PSPPH_1072 / Plasmid: pET15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48MN0
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 1.95 Å³/Da / Density % sol: 36.76 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES buffer, 0.2 M Ammonium sulfate, 27% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2008
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.83→49.8 Å / Num. all: 78827 / Num. obs: 78827 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / B_iso Wilson estimate: 29.5 Å² / R_merge(I) obs: 0.103 / Χ²: 1.7 / Net I/σ(I): 26.617
Reflection shell	Resolution: 1.83→1.86 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.795 / Mean I/σ(I) obs: 2.71 / Num. unique all: 3878 / Χ²: 1.099 / % possible all: 100

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.5.0054	refinement
PDB_EXTRACT	3.006	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.83→49.8 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.952 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 4.661 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.116 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.182	3951	5 %	RANDOM
R_work	0.149	-	-	-
all	0.151	78700	-	-
obs	0.151	78700	99.64 %	-

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 max: 50.91 Å² / B_iso mean: 17.208 Å² / B_iso min: 4.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.13 Å²	0 Å²	0 Å²
2-	-	-0.19 Å²	0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.83→49.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6648	0	4	716	7368

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	7087
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4726
X-RAY DIFFRACTION	r_angle_refined_deg	1.601	1.961	9681
X-RAY DIFFRACTION	r_angle_other_deg	0.991	3	11556
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.963	5	949
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.152	22.318	289
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.453	15	1200
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.422	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	1158
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7955
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1478
X-RAY DIFFRACTION	r_mcbond_it	1.002	1.5	4486
X-RAY DIFFRACTION	r_mcbond_other	0.322	1.5	1825
X-RAY DIFFRACTION	r_mcangle_it	1.76	2	7257
X-RAY DIFFRACTION	r_scbond_it	2.652	3	2601
X-RAY DIFFRACTION	r_scangle_it	4.275	4.5	2389

LS refinement shell

Resolution: 1.83→1.88 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	253	-
R_work	0.216	5281	-
all	-	5534	-
obs	-	5534	95.71 %

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	1.0451	-0.6679	-0.0369	1.9253	0.3194	1.2261	0.0211	0.1013	-0.1578	0.1456	0.0082	0.1032	0.1928	0.0001	-0.0293	0.0771	0.0365	-0.0138	0.0358	-0.0158	0.0397	29.8229	22.2258	21.3717
2	1.3376	0.4378	1.1663	1.3848	1.0333	2.9307	0.0862	0.002	-0.1967	0.1028	-0.0538	-0.0956	0.1818	-0.0307	-0.0324	0.0688	0.0456	-0.0247	0.047	-0.0123	0.0518	36.4898	20.1611	25.1448
3	1.1628	-0.7635	0.3508	1.319	0.1346	1.4848	-0.0722	0.0583	0.0813	0.0849	0.014	-0.206	0.0425	0.1611	0.0582	0.0305	0.0239	-0.0211	0.0503	0.0011	0.0559	39.1964	33.4604	24.656
4	0.9495	-0.3487	-0.319	0.8982	0.2037	1.487	-0.089	-0.0455	0.0023	0.1447	0.0269	-0.0759	0.0708	0.1105	0.0622	0.0451	0.0152	-0.0192	0.0339	0.0036	0.0226	30.8105	38.583	30.666
5	0.8346	-0.5902	-0.4224	1.0108	0.5414	1.1837	-0.0074	0.0087	-0.0728	0.0968	-0.0575	0.1215	0.0657	-0.0914	0.0648	0.0446	-0.0054	-0.0085	0.0437	-0.0048	0.032	18.9253	37.2292	27.6368
6	0.9123	-0.3845	0.1458	0.9187	0.6263	0.7069	-0.0012	0.0947	0.0258	-0.0615	-0.0264	-0.0232	-0.024	0.0307	0.0276	0.0464	0.0061	0.0057	0.0502	0.0124	0.0309	26.3419	39.9926	16.8216
7	9.2096	-7.6998	8.0323	6.4737	-6.7448	7.0297	-0.0377	-1.6254	-1.0509	-0.0768	1.0801	0.8297	0.0801	-1.3134	-1.0423	0.1379	-0.1418	0.0711	0.7429	0.2683	0.401	10.5899	22.4835	25.5083
8	1.9733	-0.5269	0.1328	0.7473	0.1713	0.8625	0.0345	0.0966	-0.1659	-0.0039	-0.0726	0.1304	0.059	-0.1136	0.0381	0.0494	0.0025	-0.0177	0.058	-0.019	0.0451	17.6598	29.7614	15.5753
9	0.8328	-0.6357	0.0809	1.8401	0.1624	0.915	-0.1126	-0.0515	0.2373	-0.0029	0.0342	-0.0791	-0.1739	-0.0939	0.0785	0.0866	0.0162	-0.0639	0.0245	-0.0296	0.1013	15.6919	67.6547	38.3575
10	3.5097	-0.6836	1.2764	0.4151	-0.6267	1.1963	-0.2558	-0.015	0.3771	0.0772	0.0275	-0.0701	-0.2072	0.0065	0.2282	0.1009	0.0042	-0.0939	0.036	-0.0257	0.1359	22.175	69.387	43.2146
11	2.6934	-0.5281	-0.3844	1.075	0.8616	1.8193	0.0056	-0.1986	-0.0257	0.2197	0.03	-0.087	0.0012	-0.0141	-0.0357	0.0944	0.0069	-0.0412	0.0432	-0.0177	0.0328	23.6329	55.7063	48.633
12	1.0743	-0.2652	0.0822	0.7399	0.4236	0.5832	-0.0205	0.0078	0.1133	0.0091	0.0415	-0.1583	-0.0649	0.0924	-0.0211	0.04	-0.0137	-0.0239	0.0291	-0.0061	0.0601	28.0383	53.1823	33.5456
13	1.2222	-0.4517	-0.2307	0.8258	-0.0823	1.4461	-0.0001	-0.0627	0.0653	0.0662	-0.0276	0.101	-0.1218	-0.0861	0.0278	0.0471	-0.0063	-0.0062	0.0337	-0.025	0.0434	12.9539	53.608	37.8576
14	0.7913	-0.1337	-0.0068	0.7331	0.1922	0.7081	-0.0034	0.0621	0.0154	0.0228	-0.0298	-0.0159	-0.0447	-0.0355	0.0332	0.0379	-0.0031	-0.0158	0.0269	-0.0006	0.026	17.4688	49.2807	30.5885
15	1.3575	-1.0073	1.4455	2.9768	0.1737	2.2363	-0.0968	0.3018	0.2709	-0.4272	-0.1059	-0.3391	-0.3734	0.3932	0.2027	0.1438	-0.0455	-0.0276	0.1017	0.0327	0.1307	14.5861	64.5694	22.8647
16	0.554	-0.0339	0.5821	1.0555	-0.3192	0.9687	-0.0515	0.0769	0.0593	-0.0396	-0.0869	0.0386	-0.0519	0.0071	0.1384	0.0445	0.0037	-0.0372	0.0583	-0.0195	0.0635	7.5089	57.9876	25.9943
17	1.4084	-0.1826	0.6281	1.1521	-0.3082	2.1069	-0.0521	-0.1404	0.0704	0.1438	0.0695	0.1201	-0.1271	-0.2994	-0.0174	0.0348	0.0437	0.0034	0.0888	-0.0032	0.0701	-16.8332	64.6856	20.4089
18	1.3747	-1.2377	0.3366	1.803	-0.4262	0.2642	0.0996	0.2531	-0.0248	-0.0448	-0.078	0.1813	-0.1018	-0.0689	-0.0216	0.1032	0.0993	-0.0122	0.1501	0.032	0.0619	-15.6287	61.9535	4.6406
19	0.5195	-0.311	0.0549	1.4739	0.1629	0.5982	-0.0231	0.0663	-0.0449	-0.0165	-0.0114	0.1738	-0.0126	-0.1156	0.0346	0.0077	-0.0003	-0.0149	0.061	-0.0013	0.055	-10.4244	51.5508	9.2795
20	0.7514	-0.373	0.1868	4.8143	-1.1574	1.3095	-0.0606	0.0061	0.108	0.2205	0.08	-0.1279	-0.1401	-0.0662	-0.0193	0.0283	0.0119	-0.0221	0.032	-0.0021	0.0472	-1.9444	60.7602	15.7479
21	1.1352	0.2688	0.2657	1.3756	0.3737	1.2591	-0.0074	-0.079	-0.1437	0.1769	0.0124	0.0936	0.1087	-0.0858	-0.005	0.0484	-0.0065	0.0003	0.0516	0.0054	0.0528	-4.1845	41.9707	17.8856
22	0.5538	-0.3418	-0.0591	1.1357	-0.1176	1.1637	-0.0121	0.0295	0.0979	-0.0173	-0.0037	-0.111	-0.0912	-0.0128	0.0157	0.0209	-0.0055	-0.0189	0.0312	0.0122	0.0491	2.7761	59.1297	11.3054
23	0.5881	1.0313	-0.1722	1.9426	-0.3736	0.0891	0.034	-0.0672	-0.0526	0.054	0.0422	0.071	0.0039	-0.0745	-0.0762	0.1261	-0.0541	-0.0171	0.264	0.1707	0.2388	-8.2139	44.8644	33.3604
24	1.2394	-0.2355	0.3203	0.4345	0.0079	0.938	-0.0372	-0.0819	0.0168	0.1151	0.0694	-0.0265	0.0006	-0.1314	-0.0322	0.0503	0.0128	-0.0256	0.0544	-0.01	0.0392	0.7655	57.6407	25.8997
25	2.1004	-0.2977	-0.4686	2.0022	0.9029	1.3666	-0.0425	0.2728	-0.1233	-0.2535	0.0297	-0.0822	0.0086	0.0823	0.0128	0.1022	-0.0187	0.003	0.0998	-0.0461	0.0484	8.3229	26.1523	-4.1398
26	5.9838	-2.6336	1.8919	4.2529	-0.9857	1.9757	-0.1931	0.5655	-0.0027	-0.1599	-0.0446	-0.1036	-0.0296	0.0281	0.2377	0.1146	-0.0389	-0.0222	0.1228	-0.0562	0.0726	4.1642	24.7629	-8.155
27	1.1576	-0.8329	0.1862	2.8978	2.1872	2.4449	0.1141	0.21	-0.2147	-0.3839	-0.2948	0.359	-0.1799	-0.1913	0.1808	0.2084	-0.0752	-0.048	0.1527	-0.0814	0.0971	-5.0673	26.9521	-6.5712
28	0.4702	-0.2095	-0.584	3.7825	0.1243	0.733	-0.0773	0.0942	-0.0937	-0.2055	-0.023	0.2239	0.101	-0.1069	0.1002	0.0612	-0.0397	-0.0155	0.0692	-0.0401	0.0751	0.3727	25.5393	1.5537
29	0.6549	-0.2835	-0.2543	3.0876	-0.7701	1.1094	0.0135	0.1672	-0.0838	-0.2136	-0.0386	0.119	0.0275	-0.1782	0.0251	0.0483	-0.012	-0.0282	0.0776	-0.0256	0.0416	-4.4388	38.6993	1.4744
30	0.5135	-0.4544	0.0071	1.6828	0.0413	0.7006	-0.043	0.0477	-0.0026	0.0135	0.029	-0.0873	0.029	-0.0635	0.014	0.0256	-0.0184	-0.0152	0.032	-0.0104	0.0356	3.5825	38.0266	9.3248
31	0.7929	0.7379	-0.5246	1.6937	-2.5377	4.6889	-0.0889	0.1475	-0.0544	-0.0838	0.0019	-0.156	0.0307	0.0876	0.087	0.0599	-0.0149	0.061	0.0934	0.0286	0.1642	12.4457	40.3978	-1.7138
32	0.7691	-0.665	0.4005	0.982	0.2087	1.1736	-0.0544	0.0639	0.0891	0.0191	0.0352	-0.1594	0.0117	0.1186	0.0191	0.0634	-0.0298	0.0059	0.0535	-0.0172	0.0854	15.3327	32.4585	7.8695

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 26
2	X-RAY DIFFRACTION	2	A	27 - 55
3	X-RAY DIFFRACTION	3	A	56 - 86
4	X-RAY DIFFRACTION	4	A	87 - 126
5	X-RAY DIFFRACTION	5	A	127 - 155
6	X-RAY DIFFRACTION	6	A	156 - 180
7	X-RAY DIFFRACTION	7	A	181 - 205
8	X-RAY DIFFRACTION	8	A	206 - 236
9	X-RAY DIFFRACTION	9	B	3 - 26
10	X-RAY DIFFRACTION	10	B	27 - 57
11	X-RAY DIFFRACTION	11	B	58 - 78
12	X-RAY DIFFRACTION	12	B	79 - 115
13	X-RAY DIFFRACTION	13	B	116 - 139
14	X-RAY DIFFRACTION	14	B	140 - 171
15	X-RAY DIFFRACTION	15	B	172 - 213
16	X-RAY DIFFRACTION	16	B	214 - 236
17	X-RAY DIFFRACTION	17	C	5 - 54
18	X-RAY DIFFRACTION	18	C	55 - 77
19	X-RAY DIFFRACTION	19	C	78 - 122
20	X-RAY DIFFRACTION	20	C	123 - 137
21	X-RAY DIFFRACTION	21	C	138 - 156
22	X-RAY DIFFRACTION	22	C	157 - 178
23	X-RAY DIFFRACTION	23	C	179 - 206
24	X-RAY DIFFRACTION	24	C	207 - 236
25	X-RAY DIFFRACTION	25	D	5 - 26
26	X-RAY DIFFRACTION	26	D	27 - 43
27	X-RAY DIFFRACTION	27	D	44 - 73
28	X-RAY DIFFRACTION	28	D	74 - 87
29	X-RAY DIFFRACTION	29	D	88 - 126
30	X-RAY DIFFRACTION	30	D	127 - 173
31	X-RAY DIFFRACTION	31	D	174 - 203
32	X-RAY DIFFRACTION	32	D	204 - 236

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