PDB-3rkr: Crystal structure of a metagenomic short-chain oxidoreductase (SD...

ID or keywords:

Entry

Database: PDB / ID: 3rkr

Title

Crystal structure of a metagenomic short-chain oxidoreductase (SDR) in complex with NADP

Components

Short chain oxidoreductase

Keywords

OXIDOREDUCTASE /

Rossmann fold

Function / homology

Function and homology information

oxidoreductase activity /

nucleotide binding
Similarity search - Function

Biological species

uncultured bacterium Bio5 (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.42 Å

Authors

Mayerhofer, H. / Bijtenhoorn, P. / Streit, W.R. / Mueller-Dieckmann, J.

Citation

Journal: Plos One / Year: 2011
Title: A novel metagenomic short-chain dehydrogenase/reductase attenuates Pseudomonas aeruginosa biofilm formation and virulence on Caenorhabditis elegans.
Authors: Bijtenhoorn, P. / Mayerhofer, H. / Muller-Dieckmann, J. / Utpatel, C. / Schipper, C. / Hornung, C. / Szesny, M. / Grond, S. / Thurmer, A. / Brzuszkiewicz, E. / Daniel, R. / Dierking, K. / ...

History

Deposition	Apr 18, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2012	Group: Database references
Revision 1.2	Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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	3rkr.cif.gz	340.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3rkr.ent.gz	281.9 KB	Display	PDB format
PDBx/mmJSON format	3rkr.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/rk/3rkr ftp://data.pdbj.org/pub/pdb/validation_reports/rk/3rkr	HTTPS FTP

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Related structure data

Related structure data	2ehdS S: Starting model for refinement
Similar structure data	2ehd-2 3edm-d 3tfo-d 5zmd-2 3v2h-1 4cv2-1 5xtg-1 5zmd-1 4i5f-1 4i5g-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

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

Deposited unit

A: Short chain oxidoreductase

B: Short chain oxidoreductase

C: Short chain oxidoreductase

D: Short chain oxidoreductase

hetero molecules

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

1

A: Short chain oxidoreductase

D: Short chain oxidoreductase

hetero molecules

A: Short chain oxidoreductase

D: Short chain oxidoreductase

hetero molecules

defined by author&software
113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Short chain oxidoreductase

C: Short chain oxidoreductase

hetero molecules

B: Short chain oxidoreductase

C: Short chain oxidoreductase

hetero molecules

defined by author&software
112 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	243.167, 243.167, 151.549
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

#1: Protein	Short chain oxidoreductase Mass: 27429.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium Bio5 (environmental samples) Production host: Escherichia coli (E. coli) / Strain (production host): Bl21pLysE References: UniProt: B2BKB1, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 248 / 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: 5.1 Å³/Da / Density % sol: 75.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.5 M lithium sulfate, 0.1 M citric acid, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: May 18, 2010
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8123 Å / Relative weight: 1
Reflection	Resolution: 2.42→47.7 Å / Num. all: 86188 / Num. obs: 85393 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 %
Reflection shell	Resolution: 2.42→2.55 Å / Redundancy: 5.1 % / % possible all: 95.9

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Processing

Software

Name	Version	Classification
DNA		data collection
BALBES		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EHD

2ehd

Resolution: 2.42→47.418 Å / SU ML: 0.38 / σ(F): 1.33 / Phase error: 21.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2225	4347	5.1 %	RANDOM
R_work	0.1924	-	-	-
obs	0.1939	85193	99.17 %	-
all	-	86188	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.174 Å² / k_sol: 0.368 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.0909 Å²	-0 Å²	0 Å²
2-	-	-2.0909 Å²	-0 Å²
3-	-	-	4.1818 Å²

Refinement step

Cycle: LAST / Resolution: 2.42→47.418 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6432	0	127	248	6807

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	6646
X-RAY DIFFRACTION	f_angle_d	1.624	9053
X-RAY DIFFRACTION	f_dihedral_angle_d	14.456	2311
X-RAY DIFFRACTION	f_chiral_restr	0.104	1078
X-RAY DIFFRACTION	f_plane_restr	0.008	1149

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 (%)
2.42-2.4475	0.3432	138	0.3139	2507	X-RAY DIFFRACTION	93
2.4475-2.4763	0.3151	157	0.2835	2694	X-RAY DIFFRACTION	100
2.4763-2.5065	0.3125	151	0.284	2681	X-RAY DIFFRACTION	100
2.5065-2.5382	0.3339	146	0.31	2672	X-RAY DIFFRACTION	100
2.5382-2.5716	0.2998	148	0.2908	2673	X-RAY DIFFRACTION	100
2.5716-2.6068	0.3067	140	0.2627	2695	X-RAY DIFFRACTION	100
2.6068-2.6441	0.311	143	0.2369	2698	X-RAY DIFFRACTION	100
2.6441-2.6835	0.249	141	0.2282	2686	X-RAY DIFFRACTION	100
2.6835-2.7255	0.2575	155	0.2274	2681	X-RAY DIFFRACTION	100
2.7255-2.7702	0.2554	122	0.2319	2697	X-RAY DIFFRACTION	100
2.7702-2.8179	0.2622	153	0.2138	2683	X-RAY DIFFRACTION	100
2.8179-2.8691	0.288	154	0.2205	2676	X-RAY DIFFRACTION	100
2.8691-2.9243	0.2587	159	0.214	2694	X-RAY DIFFRACTION	100
2.9243-2.984	0.2618	148	0.2201	2681	X-RAY DIFFRACTION	100
2.984-3.0489	0.2498	150	0.2134	2689	X-RAY DIFFRACTION	100
3.0489-3.1198	0.2465	146	0.2098	2691	X-RAY DIFFRACTION	100
3.1198-3.1978	0.247	139	0.22	2701	X-RAY DIFFRACTION	100
3.1978-3.2842	0.2472	145	0.2075	2698	X-RAY DIFFRACTION	100
3.2842-3.3808	0.2113	137	0.2024	2702	X-RAY DIFFRACTION	99
3.3808-3.4899	0.2362	130	0.1887	2712	X-RAY DIFFRACTION	100
3.4899-3.6146	0.2032	131	0.18	2727	X-RAY DIFFRACTION	99
3.6146-3.7593	0.2078	148	0.1812	2689	X-RAY DIFFRACTION	99
3.7593-3.9303	0.204	129	0.176	2703	X-RAY DIFFRACTION	99
3.9303-4.1374	0.2079	139	0.1661	2724	X-RAY DIFFRACTION	99
4.1374-4.3965	0.1843	156	0.1567	2680	X-RAY DIFFRACTION	99
4.3965-4.7356	0.1646	145	0.1395	2713	X-RAY DIFFRACTION	99
4.7356-5.2117	0.1547	148	0.1485	2726	X-RAY DIFFRACTION	99
5.2117-5.9645	0.2044	154	0.1807	2709	X-RAY DIFFRACTION	99
5.9645-7.5099	0.2237	155	0.2059	2751	X-RAY DIFFRACTION	98
7.5099-47.4269	0.2352	140	0.1956	2813	X-RAY DIFFRACTION	96

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	0.3501	-0.2847	0.5478	0.5325	-0.2484	1.0024	-0.1964	-0.2805	0.5386	-0.0159	-0.0395	0.491	-0.5084	-0.4933	0.0945	0.4032	0.1008	-0.0659	0.4934	0.0257	0.6082	25.4211	-57.5366	-42.6598
2	0.8714	0.0753	0.3981	0.7927	-0.3103	0.7956	-0.0559	0.2046	0.0051	0.165	0.0036	0.1487	-0.0791	-0.0063	0.0174	0.2837	-0.0149	-0.0543	0.3143	0.055	0.3603	37.7069	-69.1987	-42.5909
3	0.8648	0.0018	0.4158	0.6191	-0.391	0.7234	-0.1923	0.0908	0.5973	0.147	-0.0866	0.2285	-0.7075	0.1685	0.1597	0.5013	-0.0641	-0.1253	0.4143	0.0671	0.5338	42.9743	-53.9148	-43.6069
4	0.4885	0.3868	0.1084	0.8955	0.2054	0.6495	-0.0457	0.2006	-0.8363	-0.1901	0.2753	-0.3713	0.3672	0.4786	0.0774	0.262	0.1413	-0.0452	0.527	0.0131	0.6413	31.4208	-92.2674	-67.0433
5	1.0114	0.0058	-0.1228	0.3086	-0.178	0.9229	-0.1288	-0.0078	-0.1847	0.0907	0.0953	0.0428	0.0379	0.1247	0.0063	0.2394	0.0476	-0.0394	0.4303	0.0187	0.4201	17.2399	-84.669	-62.002
6	0.5698	0.127	0.17	0.3438	0.189	0.5155	-0.2399	0.5042	-0.4885	-0.5049	0.2609	-0.5413	0.1429	0.3168	0.0066	0.2923	-0.0107	-0.0326	0.524	-0.0872	0.5087	17.5844	-87.1974	-78.2527
7	0.8246	-0.1941	-0.1473	0.2682	0.0411	0.4839	-0.165	-0.4441	0.1775	0.2174	0.2672	0.4027	-0.2226	-0.16	-0.0307	0.2928	0.1323	0.0707	0.6111	-0.0116	0.4416	-18.2046	-76.2838	-48.7824
8	1.405	0.0419	-0.024	0.7349	0.028	0.4749	-0.1619	-0.94	-0.0602	0.465	0.2018	0.3255	0.1754	0.0931	-0.0292	0.5027	0.2388	0.0623	0.8656	0.1068	0.388	-10.8562	-83.4026	-42.3038
9	1.6038	0.048	0.2248	0.2405	-0.0458	0.3925	-0.1986	-0.1438	0.0663	0.0102	0.1376	0.1424	0.0035	0.0203	0.0058	0.2594	0.051	-0.003	0.4735	0.0617	0.3927	-2.2094	-83.9335	-57.3089
10	1.2429	-0.0373	0.0261	0.1738	-0.074	0.3054	-0.0336	0.4027	0.2376	0.1756	0.2009	0.3598	-0.1217	0.121	0.0018	0.3102	0.0028	0.008	0.5324	0.1283	0.4569	-10.1167	-79.744	-66.4574
11	1.4467	-0.1017	-0.1472	0.3041	0.03	0.3428	-0.1405	0.082	0.2365	0.1766	0.2774	0.3472	-0.1765	-0.4101	-0.0199	0.3143	0.039	0.0044	0.5613	0.0997	0.4879	-17.5122	-82.0664	-65.9466
12	0.54	-0.1861	-0.3153	0.5028	0.2094	1.3295	-0.0595	0.4943	0.9943	-0.4347	0.5295	0.4517	-0.8689	-0.0311	0.6215	0.8235	-0.1383	-0.1448	0.5068	0.4502	0.7444	58.7307	-32.2303	-50.5347
13	1.335	0.8884	0.0787	0.7184	-0.1018	0.5327	-0.0643	0.2662	0.1677	0.0412	0.0726	0.1948	-0.2861	0.0441	-0.0306	0.4336	-0.1293	-0.0699	0.3868	0.0872	0.3651	65.6196	-46.9571	-41.103
14	0.9141	0.6955	0.1384	1.0402	-0.3142	0.4205	-0.286	0.4933	0.3337	-0.1424	0.1287	0.5383	-0.4156	-0.3666	-0.0013	0.5263	-0.1207	-0.1248	0.5266	0.0998	0.5151	50.4615	-49.2606	-47.4005

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESSEQ 2:52)
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESSEQ 53:177)
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESSEQ 178:237)
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESSEQ 2:52)
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESSEQ 53:177)
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESSEQ 178:237)
7	X-RAY DIFFRACTION	7	CHAIN 'C' AND (RESSEQ 2:52)
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESSEQ 53:81)
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESSEQ 82:177)
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESSEQ 178:208)
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESSEQ 209:237)
12	X-RAY DIFFRACTION	12	CHAIN 'D' AND (RESSEQ 2:89)
13	X-RAY DIFFRACTION	13	CHAIN 'D' AND (RESSEQ 90:177)
14	X-RAY DIFFRACTION	14	CHAIN 'D' AND (RESSEQ 178:238)

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