PDB-5if3: Crystal structure of a Short-chain dehydrogenase/reductase SDR fr...

ID or keywords:

Entry

Database: PDB / ID: 5if3

Title

Crystal structure of a Short-chain dehydrogenase/reductase SDR from Burkholderia vietnamiensis

Components

Short-chain dehydrogenase/reductase SDR

Keywords

OXIDOREDUCTASE / SSGCID / Short-chain dehydrogenase/reductase SDR / dehydrogenase / reductase / SDR / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / oxidoreductase activity / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Short-chain dehydrogenase/reductase SDR

Function and homology information

Biological species

Burkholderia vietnamiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of a Short-chain dehydrogenase/reductase SDR from Burkholderia vietnamiensis
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D. / Edwards, T.E.

History

Deposition	Feb 25, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5if3.cif.gz	175.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5if3.ent.gz	138.4 KB	Display	PDB format
PDBx/mmJSON format	5if3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5if3_validation.pdf.gz	427.3 KB	Display	wwPDB validaton report
Full document	5if3_full_validation.pdf.gz	428.8 KB	Display
Data in XML	5if3_validation.xml.gz	19.3 KB	Display
Data in CIF	5if3_validation.cif.gz	28.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/if/5if3 ftp://data.pdbj.org/pub/pdb/validation_reports/if/5if3	HTTPS FTP

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Related structure data

Related structure data	1oaaS S: Starting model for refinement
Similar structure data	2xw7-d 2vok-d 2czu-d 5idq-d 4qdr-d 6hc7-1 1yo6-3 2ehd-d 2fmx-d 7aca-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	TargetTrack: SSGCID-BuviA.00010.x

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Short-chain dehydrogenase/reductase SDR

B: Short-chain dehydrogenase/reductase SDR

54.2 kDa, 2 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)	77.960, 85.780, 128.640
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-448- HOH

#1: Protein	Short-chain dehydrogenase/reductase SDR Mass: 27078.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria) Strain: G4 / LMG 22486 / Gene: Bcep1808_3729 / Plasmid: BuviA.00010.x.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JKB1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Short-chain dehydrogenase/reductase SDR

Mass: 27078.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_3729 / Plasmid: BuviA.00010.x.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JKB1

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.05 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus H1: 10% w/v PEG 20 000, 20% v/v PEG MME 550; 20mM each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine; 0.1 M MES/imidazole pH 6.5;.BuviA.00010.x.B1.PS02539 at ...Details: Morpheus H1: 10% w/v PEG 20 000, 20% v/v PEG MME 550; 20mM each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine; 0.1 M MES/imidazole pH 6.5;.BuviA.00010.x.B1.PS02539 at 20mg/ml; cryo: direct; tray 269295h1; puck wxy5-1

Crystal

Density Matthews: 1.99 Å³/Da / Density % sol: 38.05 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus H1: 10% w/v PEG 20 000, 20% v/v PEG MME 550; 20mM each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine; 0.1 M MES/imidazole pH 6.5;.BuviA.00010.x.B1.PS02539 at ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 17, 2016

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.65→40.688 Å / Num. obs: 52066 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 19.65 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.058 / Net I/σ(I): 17.88

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.65-1.69	0.471	3.62	1	100
1.69-1.74	0.376	4.54	1	99.9
1.74-1.79	0.315	5.37	1	100
1.79-1.84	0.248	6.77	1	99.9
1.84-1.91	0.179	8.7	1	99.9
1.91-1.97	0.153	10.57	1	99.9
1.97-2.05	0.116	13.11	1	99.9
2.05-2.13	0.095	15.56	1	100
2.13-2.22	0.078	18.29	1	99.9
2.22-2.33	0.076	19.36	1	99.9
2.33-2.46	0.063	23.06	1	100
2.46-2.61	0.057	25.32	1	100
2.61-2.79	0.052	29.06	1	99.9
2.79-3.01	0.05	30.83	1	100
3.01-3.3	0.046	33.86	1	100
3.3-3.69	0.042	36.99	1	100
3.69-4.26	0.041	38.42	1	99.9
4.26-5.22	0.039	40.12	1	99.8
5.22-7.38	0.04	38.76	1	99.6
7.38-40.688	0.038	38.42	1	96.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.5 Å	19.67 Å
Translation	3.5 Å	19.67 Å

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Processing

Software

Name	Version	Classification
PHENIX	dev_2328	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1oaa

1oaa

Resolution: 1.65→40.688 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.89

	R_factor	Num. reflection	% reflection
R_free	0.1807	2603	5 %
R_work	0.1551	-	-
obs	0.1564	52055	99.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 99.86 Å² / B_iso mean: 32.0759 Å² / B_iso min: 11.92 Å²

Refinement step

Cycle: final / Resolution: 1.65→40.688 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3012	0	0	315	3327
B_iso mean	-	-	-	39.99	-
Num. residues	-	-	-	-	425

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3094
X-RAY DIFFRACTION	f_angle_d	0.758	4246
X-RAY DIFFRACTION	f_chiral_restr	0.051	526
X-RAY DIFFRACTION	f_plane_restr	0.006	558
X-RAY DIFFRACTION	f_dihedral_angle_d	9.305	1871

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.65-1.68	0.2685	141	0.2254	2551	2692	100
1.68-1.7123	0.2416	136	0.2002	2592	2728	100
1.7123-1.7473	0.2226	127	0.1875	2564	2691	100
1.7473-1.7853	0.2234	152	0.1768	2589	2741	100
1.7853-1.8268	0.2187	134	0.1628	2555	2689	100
1.8268-1.8725	0.183	133	0.1578	2590	2723	100
1.8725-1.9231	0.2148	134	0.1722	2584	2718	100
1.9231-1.9797	0.1988	140	0.1591	2580	2720	100
1.9797-2.0436	0.2023	124	0.1613	2609	2733	100
2.0436-2.1167	0.2028	136	0.1521	2569	2705	100
2.1167-2.2014	0.1907	142	0.143	2575	2717	100
2.2014-2.3016	0.1797	147	0.1557	2603	2750	100
2.3016-2.4229	0.2073	141	0.151	2601	2742	100
2.4229-2.5747	0.1766	113	0.1548	2604	2717	100
2.5747-2.7734	0.1946	128	0.1583	2645	2773	100
2.7734-3.0525	0.1878	139	0.1658	2618	2757	100
3.0525-3.4939	0.1887	142	0.1549	2618	2760	100
3.4939-4.4012	0.1523	141	0.1382	2667	2808	100
4.4012-40.7004	0.1394	153	0.1466	2738	2891	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	2.65	0.5201	-0.5497	3.4887	-0.8067	3.3869	0.0758	-0.0381	0.1144	0.0873	-0.0564	-0.025	-0.2311	0.1699	0.0472	0.1608	-0.0457	-0.0051	0.1494	0.0045	0.2462	21.7157	50.5793	32.9083
2	2.0947	0.7631	-0.4785	2.906	-1.405	4.1777	0.2079	-0.3078	0.1224	0.5873	-0.318	-0.2533	-0.511	0.1449	-0.024	0.2977	-0.0941	-0.0161	0.2164	-0.0052	0.2876	21.1935	53.3381	37.7125
3	1.4151	0.9063	-0.9804	4.0269	-2.1603	2.8499	0.1368	-0.134	0.1958	0.7705	0.0257	0.1956	-0.4002	-0.0781	-0.1666	0.3381	-0.0318	0.0716	0.1952	-0.0428	0.2263	15.346	51.7643	43.1667
4	1.272	0.2946	0.3024	3.6244	-1.0183	3.7761	0.076	0.0561	0.3915	0.1355	-0.086	0.4736	-0.3508	-0.2845	0.0026	0.163	-0.0064	0.025	0.1799	0.0008	0.3105	10.0796	48.1416	33.2717
5	1.0976	-0.205	0.5497	1.2227	-0.7726	1.7806	0.0228	-0.2705	0.1104	0.745	-0.3413	-0.4283	-0.4426	0.5625	0.2765	0.3203	-0.0973	-0.1083	0.296	0.0717	0.2253	24.1995	34.7233	53.2623
6	1.3833	0.3169	0.1685	2.2312	-0.8956	1.7501	0.0225	0.0096	-0.0888	0.1259	-0.1453	-0.1438	-0.0149	0.224	0.1307	0.1086	-0.0063	0.0122	0.1471	0.0093	0.1694	17.468	33.5212	38.2293
7	2.6506	1.2796	-0.7771	4.0397	-1.3716	2.0753	-0.0176	0.0385	0.0468	0.0101	-0.0881	0.0001	0.007	0.1626	0.0307	0.1348	0.0152	0.0371	0.1401	-0.0118	0.1848	14.7985	31.6915	32.9898
8	6.9424	-0.4987	-0.7473	2.1392	-2.2949	5.8018	-0.2225	-0.0206	-1.142	-0.1443	-0.0893	0.1033	1.2084	-0.4188	0.239	0.512	-0.0362	0.1169	0.2662	0.0547	0.4112	12.0322	5.8303	55.3397
9	3.5666	0.116	2.5908	4.295	-0.3317	4.2434	0.0832	-0.0575	-0.5687	-0.2027	-0.1695	-0.4996	1.0673	0.3003	0.0505	0.4127	0.1104	0.1131	0.2763	0.1026	0.3353	20.8698	7.7411	49.3588
10	2.5727	-0.0058	1.0983	3.1694	-0.3573	5.1849	-0.1326	-0.3682	-0.5601	0.7408	-0.0957	0.3314	0.2998	-0.2941	0.0832	0.4456	-0.0037	0.1465	0.3542	0.124	0.292	9.1515	12.4942	63.5528
11	2.732	0.2894	-0.1287	4.4722	-0.4741	2.553	-0.0646	-0.5118	-0.0929	0.5612	0.1627	0.8651	-0.089	-0.7799	-0.1688	0.5349	0.0453	0.1918	0.4764	0.0981	0.3405	5.5763	18.2153	66.1153
12	1.9987	-0.2889	2.398	1.1132	-0.4443	2.8968	0.0682	-0.8172	-0.5102	0.8301	0.0512	0.59	-0.196	-0.6747	-0.3098	0.6634	0.0931	0.227	0.678	0.1281	0.3156	5.0881	16.5325	71.7587
13	0.8132	-0.2507	-0.0135	2.2288	-1.0603	2.1733	-0.0846	-0.3452	-0.0951	0.725	0.1022	0.1746	-0.2577	-0.0645	0.0283	0.3344	0.0132	0.0636	0.2383	0.0163	0.167	11.3472	27.0437	57.075
14	1.2317	-0.4962	0.6644	2.6927	-1.0756	3.3423	0.0089	-0.2526	-0.1915	0.5395	-0.0345	-0.1735	0.0215	0.2538	0.0625	0.2308	0.0049	-0.0071	0.2229	0.0561	0.1864	18.5778	20.3872	54.3871
15	2.329	-0.6989	1.2293	3.2116	-1.2063	3.1038	-0.0428	-0.1012	-0.059	0.2146	-0.1639	-0.2379	0.063	0.2357	0.1335	0.1583	-0.0014	0.0284	0.1767	0.0368	0.1907	19.5317	22.7697	46.5554
16	2.4846	1.7588	-0.4489	3.9266	-0.7339	2.3884	0.0209	-0.2205	0.004	0.3007	-0.3252	-0.2715	0.5621	0.3735	0.2528	0.1413	0.0705	0.0025	0.2391	0.0755	0.2638	23.1821	18.2612	50.2387
17	4.2736	-0.0392	2.9044	3.2432	1.5846	7.0972	-0.2287	0.5549	0.1045	-0.2908	0.1427	-0.8151	-0.2125	0.931	0.0606	0.138	-0.0117	0.0622	0.2366	0.0331	0.3281	28.1234	42.0795	27.7431
18	4.0866	0.3149	0.6945	2.9954	-1.6306	2.9168	0.1048	0.3545	-0.3933	-0.7019	-0.3642	-0.683	0.5856	0.5824	0.2024	0.2751	0.0216	0.1104	0.2476	-0.0144	0.2743	22.6991	32.152	26.1784

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 6 through 31 )	A	6 - 31
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 46 )	A	32 - 46
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 73 )	A	47 - 73
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 74 through 91 )	A	74 - 91
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 92 through 118 )	A	92 - 118
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 119 through 174 )	A	119 - 174
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 175 through 223 )	A	175 - 223
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 224 through 236 )	A	224 - 236
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 237 through 252 )	A	237 - 252
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 8 through 32 )	B	8 - 32
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 33 through 46 )	B	33 - 46
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 47 through 59 )	B	47 - 59
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 60 through 118 )	B	60 - 118
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 119 through 155 )	B	119 - 155
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 156 through 174 )	B	156 - 174
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 175 through 223 )	B	175 - 223
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 224 through 236 )	B	224 - 236
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 237 through 251 )	B	237 - 251

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi