PDB-5va8: Crystal Structure of Short-chain dehydrogenase/reductase SDR from...

ID or keywords:

Entry

Database: PDB / ID: 5va8

Title

Crystal Structure of Short-chain dehydrogenase/reductase SDR from Burkholderia phymatum in complex with NADP

Components

Short-chain dehydrogenase/reductase SDR

Keywords

OXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / NADP / SDR

Function / homology

Function and homology information

nucleotide binding
Similarity search - Function

Biological species

Paraburkholderia phymatum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal Structure of Short-chain dehydrogenase/reductase SDR from Burkholderia phymatum in complex with NADP
Authors: Delker, S.L. / Edwards, T.E. / Lorimer, D.

History

Deposition	Mar 24, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.SG_entry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5va8.cif.gz	420.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5va8.ent.gz	345.2 KB	Display	PDB format
PDBx/mmJSON format	5va8.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/va/5va8 ftp://data.pdbj.org/pub/pdb/validation_reports/va/5va8	HTTPS FTP

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Related structure data

Related structure data	5idxS S: Starting model for refinement
Similar structure data	5idx-1 5idy-1 4h16-1 3vdq-d 2bgk-1 2q2q-1 5itw-d 2q2w-d 3ai2-1 3w8f-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-BuphA.00010.g

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Short-chain dehydrogenase/reductase SDR

B: Short-chain dehydrogenase/reductase SDR

C: Short-chain dehydrogenase/reductase SDR

D: Short-chain dehydrogenase/reductase SDR

hetero molecules

116 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)	133.560, 75.130, 109.880
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Short-chain dehydrogenase/reductase SDR Mass: 27776.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria) Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_2062 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2JE32
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid Mass: 250.186 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₅O₆P
#4: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1293 / 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: 2.48 Å³/Da / Density % sol: 50.42 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus G5: 10% Peg 20K, 20% Peg MME, 0.2M carboxylic (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium l-tartrate, 0.2 M sodium oxamate), 0.1 M MOPS/Hepes, pH 7.5

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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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.6→44.35 Å / Num. obs: 145542 / % possible obs: 99.7 % / Redundancy: 6.15 % / CC_1/2: 0.99 / R_merge(I) obs: 0.055 / Net I/σ(I): 19.54
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 6.17 % / R_merge(I) obs: 0.46 / Num. unique obs: 10685 / CC_1/2: 0.92 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2689: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IDX

5idx

Resolution: 1.6→44.348 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1774	1928	1.33 %
R_work	0.1486	-	-
obs	0.149	145496	99.67 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→44.348 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7482	0	295	1293	9070

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8065
X-RAY DIFFRACTION	f_angle_d	0.834	11068
X-RAY DIFFRACTION	f_dihedral_angle_d	13.592	4916
X-RAY DIFFRACTION	f_chiral_restr	0.053	1284
X-RAY DIFFRACTION	f_plane_restr	0.006	1548

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 (%)
1.6-1.64	0.2443	148	0.2062	10143	X-RAY DIFFRACTION	100
1.64-1.6844	0.2494	131	0.1979	10196	X-RAY DIFFRACTION	100
1.6844-1.7339	0.2117	141	0.1834	10159	X-RAY DIFFRACTION	100
1.7339-1.7899	0.2067	132	0.167	10223	X-RAY DIFFRACTION	100
1.7899-1.8539	0.2374	126	0.1613	10159	X-RAY DIFFRACTION	100
1.8539-1.9281	0.1788	143	0.1549	10238	X-RAY DIFFRACTION	100
1.9281-2.0159	0.1918	161	0.1633	10165	X-RAY DIFFRACTION	100
2.0159-2.1221	0.1799	113	0.1552	10243	X-RAY DIFFRACTION	100
2.1221-2.2551	0.1846	128	0.1449	10253	X-RAY DIFFRACTION	100
2.2551-2.4292	0.1656	143	0.144	10232	X-RAY DIFFRACTION	100
2.4292-2.6736	0.1772	138	0.1466	10256	X-RAY DIFFRACTION	100
2.6736-3.0604	0.206	140	0.1492	10277	X-RAY DIFFRACTION	99
3.0604-3.8555	0.1574	135	0.1355	10372	X-RAY DIFFRACTION	99
3.8555-44.3646	0.1407	149	0.1319	10652	X-RAY DIFFRACTION	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	2.6277	0.0994	1.7808	1.3111	-0.8696	3.8443	0.0086	0.0977	-0.4176	0.002	-0.007	-0.1699	0.1659	0.0965	0.0041	0.1491	-0.0022	0.0022	0.0559	-0.0273	0.2216	-47.6573	-25.6789	-20.9164
2	2.4862	-2.8044	0.0519	5.4819	-0.5272	0.4049	-0.0271	0.1153	-0.4602	0.1589	-0.0032	0.1864	0.1394	-0.0327	0.0409	0.1585	-0.0216	-0.0049	0.0925	-0.0368	0.258	-56.5787	-28.711	-24.0818
3	0.8689	-0.0343	0.1728	0.578	-0.0381	0.7716	0.0089	0.0514	-0.0579	-0.0185	-0.0134	0.0661	-0.0003	-0.0137	0.0072	0.1182	-0.006	-0.0009	0.0752	-0.0222	0.1021	-51.0518	-9.229	-24.1889
4	8.8397	-1.3767	-3.1415	8.1355	-4.1721	7.9087	1.0029	0.7759	0.2513	-1.2861	-0.5999	0.6185	0.1351	-1.1505	-0.3657	0.4563	0.1385	-0.0546	0.5809	-0.1445	0.3178	-48.9772	-17.7356	-47.7343
5	7.5914	2.8417	5.4058	4.5049	3.1645	4.3723	0.1377	0.4922	-0.1257	0.2289	-0.4676	0.3087	0.6995	0.19	0.2088	0.3791	0.0113	0.028	0.5428	-0.1627	0.2121	-40.1044	-18.5551	-50.5004
6	1.0362	0.1893	-0.3572	0.8163	-0.3361	2.92	-0.0031	0.1522	-0.1757	-0.0607	-0.0084	-0.0418	0.1493	0.0477	0.0138	0.0872	0.015	-0.003	0.1121	-0.0377	0.1319	-35.9186	-15.9513	-26.9845
7	3.5579	0.9025	1.2304	2.7482	1.0848	3.0501	0.0281	-0.0814	-0.4307	0.1073	-0.0134	0.0111	0.2259	0.0005	-0.0233	0.1374	0.0155	0.0032	0.0927	0.0357	0.2043	-18.9325	-24.0107	-17.5982
8	1.9881	1.7839	0.1391	8.9073	-2.8025	3.0076	0.0753	-0.1683	-0.4247	0.3029	-0.069	-0.2537	0.1668	0.1625	0.0092	0.1456	0.0509	-0.0142	0.1863	0.0341	0.2495	-9.9479	-24.2648	-13.1715
9	9.238	0.5124	-0.2266	0.7349	-0.2489	1.5661	0.0293	0.2124	-0.4161	-0.0158	-0.0177	-0.1864	0.0708	0.2113	-0.0148	0.1149	0.0105	0.0121	0.1569	-0.0139	0.1696	-8.8727	-19.5404	-25.9254
10	1.2679	2.3812	1.487	7.9185	4.5674	3.6964	-0.0507	0.1484	-0.0734	-0.2492	0.0819	-0.2719	-0.201	0.1913	-0.0659	0.085	0.0171	-0.0051	0.1751	0.0317	0.1429	-11.5216	-4.5942	-24.0762
11	1.4041	0.0143	-0.0261	1.6489	0.3194	0.8898	0.0012	0.1147	-0.0806	-0.0443	-0.0269	-0.0766	0.003	0.0404	0.0257	0.0739	0.0025	-0.0014	0.1116	0.0057	0.0892	-22.4853	-8.2703	-24.4951
12	4.4771	-0.551	-2.3495	6.8306	4.9504	4.4595	-0.1184	-0.0248	0.3145	0.597	1.2588	-1.1499	0.1009	1.9228	-1.023	0.3735	0.0426	-0.0944	0.4547	-0.1579	0.367	-19.0409	-2.9041	0.878
13	6.7976	3.4399	5.3965	1.9448	2.8127	4.2856	0.4334	-0.7065	0.2679	0.2237	-0.3678	0.0692	0.5218	-0.651	-0.0079	0.3407	-0.0445	0.0016	0.2745	-0.1008	0.2571	-27.654	-2.7256	3.1212
14	3.5617	-1.7496	-1.9132	1.7173	2.551	6.4746	-0.088	-0.1637	-0.1504	0.1955	0.0496	-0.0523	0.2124	0.1865	0.0409	0.1165	-0.0342	-0.0063	0.0688	0.027	0.1272	-29.7739	-14.6015	-11.9191
15	1.1369	-0.5965	-0.466	0.7447	0.8418	1.937	0.0176	0.1243	-0.0769	-0.0335	-0.0288	0.0368	-0.0047	-0.063	0.0329	0.1175	-0.0169	-0.0057	0.1357	-0.0033	0.1291	-32.3033	-11.2626	-23.5839
16	4.6175	0.3313	-2.1422	1.7191	-0.816	3.657	0.0455	0.2541	0.4261	-0.1098	-0.048	-0.2352	-0.2202	0.1505	0.0204	0.1606	-0.0107	0.006	0.1141	0.0603	0.1862	-46.0848	26.3917	-37.1375
17	4.6939	0.5195	-1.8264	1.8135	-1.1907	3.4703	0.0132	0.1224	0.3399	-0.0159	-0.0058	-0.0365	-0.1191	0.1403	-0.0406	0.1305	-0.0144	0.0037	0.0592	0.0065	0.1441	-50.9024	26.8319	-31.7719
18	4.3375	3.68	-0.1897	7.5002	-0.3666	1.1865	-0.0318	0.094	0.3642	-0.1291	-0.0024	0.1429	-0.089	0.021	0.0371	0.1234	0.0087	-0.0065	0.0792	0.0285	0.164	-57.8675	29.299	-30.9269
19	0.8303	-0.0636	0.0069	0.6935	-0.0418	0.4827	0.0145	0.1107	0.0131	-0.0145	-0.0249	0.0559	0.0025	0.0241	0.0097	0.1293	-0.005	-0.0038	0.106	-0.009	0.1049	-51.4929	10.0129	-30.9034
20	8.3033	1.7233	1.2017	7.8703	-3.3467	3.0725	0.3382	-0.5024	-0.134	1.1857	-0.4191	0.5217	0.1846	-1.3028	0.0636	0.4394	-0.0907	0.0725	0.414	-0.1429	0.2961	-49.7227	18.9357	-7.0967
21	7.3069	-4.0431	-6.0029	5.5672	3.9668	5.1016	-0.1118	-0.5612	0.0939	-0.0056	-0.1658	0.0564	-0.1575	0.5863	0.2017	0.2985	-0.0279	-0.0366	0.3206	-0.041	0.1472	-40.5788	20.3156	-4.5125
22	2.215	-0.4771	1.6453	1.2198	0.9765	8.3321	-0.0807	0.0137	0.2614	0.0515	-0.0872	-0.0297	-0.3688	0.0364	0.203	0.1068	-0.0442	0.0031	0.0879	0.02	0.14	-38.073	22.3283	-23.8582
23	1.0932	-0.4898	0.6441	0.5837	-0.0847	1.0208	0.0088	0.1716	0.0931	-0.0453	-0.0697	-0.109	-0.0688	0.1368	0.0609	0.1018	-0.0214	0.0095	0.1322	0.0146	0.1048	-35.3226	12.8346	-31.3705
24	2.6326	-0.912	-1.5758	3.3566	1.3745	3.0999	0.0433	0.3129	0.401	-0.1479	-0.0436	-0.0121	-0.2108	0.063	-0.0012	0.1594	-0.0348	-0.0038	0.1961	0.1186	0.228	-19.9823	26.206	-37.3261
25	0.9258	-0.4629	-0.755	3.7958	-2.0801	3.3065	0.1128	0.3345	0.5598	-0.2553	-0.0915	-0.279	-0.1925	0.0381	-0.0495	0.2067	-0.0608	0.0179	0.3207	0.1531	0.3328	-11.0676	26.9947	-41.5644
26	0.9078	-0.0586	-0.0187	0.9993	0.0318	0.6845	0.0142	0.0922	0.0978	-0.0226	-0.0695	-0.1699	0.0036	0.0819	0.0459	0.0948	-0.0117	0.0045	0.1616	0.0459	0.1256	-16.5842	11.0931	-30.377
27	2.388	2.4441	3.4771	4.346	6.2206	9.1266	-0.3043	-0.0919	-0.5336	-0.9685	1.4439	-1.6419	-0.2058	2.0319	-1.1529	0.4271	-0.0283	0.161	0.7144	-0.106	0.5072	-18.6132	4.3745	-55.4294
28	6.9278	-3.1402	-3.9892	3.0202	2.6443	5.1609	0.2557	1.1003	-0.4569	-0.5334	-0.2627	-0.125	-0.0346	-0.6073	0.0136	0.4281	0.0267	0.053	0.429	-0.1075	0.2851	-27.2224	3.7578	-57.8335
29	1.7019	0.427	0.106	3.0174	3.7438	7.5794	0.0078	0.2994	0.1498	-0.231	-0.0533	-0.0839	-0.1419	0.1641	0.0432	0.127	0.0218	0.0108	0.1966	0.0783	0.1315	-30.345	16.2585	-43.0712
30	0.6208	0.0322	0.0856	0.4424	0.6451	1.4056	0.0089	0.1339	0.0868	-0.0291	-0.0417	0.0108	0.0078	-0.0103	0.0388	0.1552	-0.0057	0.0022	0.1979	0.0284	0.1525	-32.8032	12.8639	-31.3937

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 68 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 188 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 189 through 202 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 203 through 216 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 217 through 259 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -1 through 40 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 41 through 68 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 69 through 87 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 88 through 130 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 131 through 188 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 189 through 202 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 203 through 216 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 217 through 235 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 236 through 259 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid -1 through 17 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 18 through 40 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 41 through 68 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 69 through 188 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 189 through 202 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 203 through 216 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 217 through 235 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 236 through 259 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid -1 through 40 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 41 through 68 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 69 through 188 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 189 through 202 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 203 through 216 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 217 through 235 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 236 through 259 )

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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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