PDB-5u4s: Crystal structure of a Short chain dehydrogenase from Burkholderi...

ID or keywords:

Entry

Database: PDB / ID: 5u4s

Title

Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP.

Components

Putative short chain dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / dehydrogenase / structural genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding / cytosol
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.4 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 6, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5u4s.cif.gz	197.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5u4s.ent.gz	157.4 KB	Display	PDB format
PDBx/mmJSON format	5u4s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5u4s_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5u4s_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5u4s_validation.xml.gz	23.7 KB	Display
Data in CIF	5u4s_validation.cif.gz	35.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u4/5u4s ftp://data.pdbj.org/pub/pdb/validation_reports/u4/5u4s	HTTPS FTP

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Related structure data

Related structure data	5u2wC C: citing same article (ref.)
Similar structure data	3nye-d 5mpt-d 3vx1-d 7meu-d 3p94-6 5evy-d 6yqa-1 5om6-1 4ga7-2 1uhg-2 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-BuceA.00010.y

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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: Putative short chain dehydrogenase

B: Putative short chain dehydrogenase

hetero molecules

53.9 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)	39.270, 75.660, 146.010
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative short chain dehydrogenase Mass: 26023.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria) Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610 Gene: BCAM2128 / Plasmid: BuceA.00010.y.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EFS5
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-BEZ / BENZOIC ACID Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.09 Å³/Da / Density % sol: 41.1 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: RigakuReagents JCSG+ screen C6: 40% PEG 300, 100mM Sodium phosphate dibasic / citric acid pH 4.20: BuceA.00010.g.B1.PS01748 at 23.45mg/ml + 5mM NADP: cryo: direct: tray 285429c6, puck izz8-4. ...Details: RigakuReagents JCSG+ screen C6: 40% PEG 300, 100mM Sodium phosphate dibasic / citric acid pH 4.20: BuceA.00010.g.B1.PS01748 at 23.45mg/ml + 5mM NADP: cryo: direct: tray 285429c6, puck izz8-4. For phasing a crystal from the same condition was incubated in reservoir with 10% 5M NaI in EG, with a final concentrations of 10% EG and 500mM NaI, for 30sec and flash frozen. Phasing data were collected at CuKa

Crystal

Density Matthews: 2.09 Å³/Da / Density % sol: 41.1 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop
Details: RigakuReagents JCSG+ screen C6: 40% PEG 300, 100mM Sodium phosphate dibasic / citric acid pH 4.20: BuceA.00010.g.B1.PS01748 at 23.45mg/ml + 5mM NADP: cryo: direct: tray 285429c6, puck izz8-4. ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-G		1	0.97856
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Nov 29, 2016
RIGAKU SATURN 944+	2	CCD	Nov 29, 2016

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Diamond [111]	SINGLE WAVELENGTH	M	x-ray	1
2	RIGAKU VARIMAX	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97856	1
2	1.5418	1

Reflection

Resolution: 1.4→50 Å / Num. obs: 86241 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.734 % / B_iso Wilson estimate: 12.61 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.072 / Net I/σ(I): 13.91

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
1.4-1.44	3.605	0.542	2.12	0.753	1	94.7
1.44-1.48	4.542	0.46	3	0.853	1	98.9
1.48-1.52	5.249	0.364	4.18	0.919	1	100
1.52-1.57	5.998	0.292	5.66	0.959	1	100
1.57-1.62	6.086	0.252	6.57	0.966	1	100
1.62-1.67	6.114	0.211	7.82	0.977	1	100
1.67-1.74	6.115	0.173	9.4	0.984	1	100
1.74-1.81	6.117	0.14	11.39	0.987	1	100
1.81-1.89	6.132	0.117	13.55	0.991	1	100
1.89-1.98	6.12	0.096	16.08	0.993	1	100
1.98-2.09	6.124	0.081	18.82	0.995	1	100
2.09-2.21	6.123	0.072	21.07	0.995	1	100
2.21-2.37	6.107	0.065	23.14	0.996	1	100
2.37-2.56	6.113	0.06	24.78	0.996	1	100
2.56-2.8	6.093	0.058	26.14	0.995	1	100
2.8-3.13	6.063	0.055	27.71	0.997	1	100
3.13-3.61	6.034	0.051	29.62	0.997	1	100
3.61-4.43	5.958	0.051	30.82	0.996	1	100
4.43-6.26	5.814	0.051	30.42	0.997	1	99.9
6.26-50	5.165	0.051	28.66	0.996	1	98.4

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
ARP		model building
Coot		model building
PHENIX	(dev_2608)	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.4→50 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.82

	R_factor	Num. reflection	% reflection
R_free	0.1662	1984	2.3 %
R_work	0.1482	-	-
obs	0.1487	86226	99.51 %

Solvent computation

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

Displacement parameters

B_iso max: 88.9 Å² / B_iso mean: 19.6795 Å² / B_iso min: 6.73 Å²

Refinement step

Cycle: final / Resolution: 1.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3328	0	119	450	3897
B_iso mean	-	-	13.32	31.56	-
Num. residues	-	-	-	-	467

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3666
X-RAY DIFFRACTION	f_angle_d	1.076	5049
X-RAY DIFFRACTION	f_chiral_restr	0.087	619
X-RAY DIFFRACTION	f_plane_restr	0.007	695
X-RAY DIFFRACTION	f_dihedral_angle_d	14.623	1439

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.4-1.435	0.2548	159	0.2359	5580	95
1.435-1.4738	0.2411	131	0.2053	5905	99
1.4738-1.5172	0.1924	138	0.1771	6003	100
1.5172-1.5662	0.1795	151	0.1548	5944	100
1.5662-1.6221	0.1761	126	0.1533	5981	100
1.6221-1.6871	0.1674	123	0.1442	6011	100
1.6871-1.7639	0.1487	134	0.1413	6014	100
1.7639-1.8568	0.1341	161	0.1406	6003	100
1.8568-1.9732	0.1714	135	0.1448	6037	100
1.9732-2.1255	0.17	140	0.1408	6027	100
2.1255-2.3394	0.1473	162	0.1392	6048	100
2.3394-2.6778	0.1751	141	0.1438	6103	100
2.6778-3.3734	0.1847	151	0.1513	6160	100
3.3734-50	0.1413	132	0.14	6426	100

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	1.0126	-0.3293	-0.2487	1.3657	-0.2518	3.1768	-0.0324	-0.187	-0.0316	0.2355	0.0952	0.057	-0.13	-0.2432	-0.0594	0.1353	0.0207	0.0066	0.1297	0.0196	0.0849	21.9083	31.0809	47.0483
2	0.6964	-0.0432	-0.0035	1.0378	-0.0781	1.8906	-0.0024	-0.0112	-0.0063	0.1149	0.0195	-0.027	-0.09	-0.0663	-0.0144	0.0737	0.0073	0.0059	0.0633	0.013	0.0871	26.3945	34.2555	30.2811
3	1.3649	-0.0885	-1.0482	0.5866	-0.5058	2.2628	-0.1491	-0.0311	-0.2905	0.0851	0.0332	-0.1533	0.3664	0.0681	0.0852	0.1593	0.0026	-0.0105	0.0974	0.0151	0.1877	34.9895	22.8112	31.9815
4	1.7235	1.5124	-0.0638	3.8497	0.6395	5.4575	-0.0549	0.1494	-0.0917	-0.0393	0.0077	-0.0839	0.3535	0.2573	-0.0244	0.0763	0.0471	-0.0102	0.1475	0.0273	0.0676	29.8894	42.5601	-1.7128
5	2.0343	-1.8103	-0.4939	5.0448	4.8248	7.8133	0.2042	0.3316	0.1579	-0.4083	-0.0023	-0.1965	-0.5049	0.1215	-0.1503	0.1024	0.0034	0.0271	0.1306	0.0333	0.0996	33.1234	48.7644	-1.7745
6	1.9121	0.8037	-1.137	1.4154	-0.9645	5.0167	0.2464	0.0578	0.2456	-0.176	-0.0139	0.1397	-0.5896	-0.3059	-0.2038	0.1835	0.045	0.0231	0.1952	0.0128	0.1161	24.4441	48.3415	-4.0332
7	0.4354	0.1841	-0.6834	0.5964	-0.7431	4.3718	0.0545	0.229	0.0604	-0.1197	0.0362	0.1452	-0.1357	-0.662	-0.1085	0.1073	0.0348	-0.0086	0.2507	0.0201	0.1347	15.9145	42.9265	3.5418
8	0.645	-0.0235	0.0275	1.0649	0.1019	2.8504	-0.0047	-0.0029	0.0745	0.0763	0.0358	0.0145	-0.2404	-0.1099	-0.0151	0.0697	0.0154	0.0107	0.0744	0.0145	0.0953	25.0385	44.7346	17.8599
9	0.8231	0.0941	0.2727	0.6762	-0.2684	1.8299	0.0051	0.0987	-0.0706	-0.101	0.0185	-0.0218	0.0944	-0.0283	-0.0284	0.0854	0.0016	0.0091	0.0963	-0.0019	0.1034	28.6262	34.7286	12.6218
10	3.2249	0.9716	0.1498	2.8284	0.0151	2.2198	0.0286	-0.0743	0.2353	0.2087	0.0169	-0.2826	-0.1843	0.1506	-0.0421	0.0888	-0.0156	-0.0033	0.1003	0.0192	0.0779	37.2032	47.2565	12.6012
11	4.4765	0.8805	1.0528	2.0502	-0.1297	3.8037	-0.0884	0.3298	-0.1283	-0.5094	0.0721	-0.3177	0.05	0.3949	0.0106	0.1556	0.0162	0.0396	0.2026	0.0266	0.1505	40.1232	42.8399	2.2798
12	2.5669	-1.0706	1.3664	1.2607	-1.3498	3.8345	-0.0156	0.1478	0.0462	-0.0345	-0.1194	-0.1587	-0.1364	0.1323	0.118	0.0724	0.0048	0.014	0.142	0.0328	0.144	44.7998	38.1266	15.6282
13	5.5979	-0.6197	-1.3125	6.1261	-0.9555	5.9523	-0.1893	-0.6125	1.3372	0.4237	-0.0671	-0.4264	-0.9017	0.4077	0.0376	0.2166	-0.0222	-0.0934	0.2123	-0.0601	0.3771	45.3307	40.2098	31.3868

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 1 through 83 )	A	1 - 83
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 84 through 165 )	A	84 - 165
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 166 through 236 )	A	166 - 236
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 15 )	B	1 - 15
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 16 through 27 )	B	16 - 27
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 28 through 49 )	B	28 - 49
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 50 through 69 )	B	50 - 69
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 70 through 105 )	B	70 - 105
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 106 through 165 )	B	106 - 165
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 166 through 191 )	B	166 - 191
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 192 through 204 )	B	192 - 204
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 205 through 225 )	B	205 - 225
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 226 through 237 )	B	226 - 237

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