PDB-6dbb: Crystal structure of a Putative aldehyde dehydrogenase family pro...

ID or keywords:

Entry

Database: PDB / ID: 6dbb

Title

Crystal structure of a Putative aldehyde dehydrogenase family protein Burkholderia cenocepacia J2315 in complex with partially reduced NADH

Components

Putative aldehyde dehydrogenase family protein

Keywords

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

Function / homology

Function and homology information

oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of a Putative aldehyde dehydrogenase family protein Burkholderia cenocepacia J2315 in complex with partially reduced NADH
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	May 2, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6dbb.cif.gz	608.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6dbb.ent.gz	498.1 KB	Display	PDB format
PDBx/mmJSON format	6dbb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6dbb_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	6dbb_full_validation.pdf.gz	2.3 MB	Display
Data in XML	6dbb_validation.xml.gz	64.2 KB	Display
Data in CIF	6dbb_validation.cif.gz	95 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/db/6dbb ftp://data.pdbj.org/pub/pdb/validation_reports/db/6dbb	HTTPS FTP

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Related structure data

Similar structure data	2112 2118 2122 2109 2115 6rtr-d 3p14-2 3627 3623 3631 Search similar-shape structures by Omokage search (details) 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
Other databases	TargetTrack: SSGCID-BuceA.00020.r

Similar structure data

Other databases

TargetTrack: SSGCID-BuceA.00020.r

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (5) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (5)

Deposited unit

A: Putative aldehyde dehydrogenase family protein

B: Putative aldehyde dehydrogenase family protein

C: Putative aldehyde dehydrogenase family protein

hetero molecules

171 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative aldehyde dehydrogenase family protein

hetero molecules

A: Putative aldehyde dehydrogenase family protein

hetero molecules

defined by author&software
Evidence: gel filtration
114 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative aldehyde dehydrogenase family protein

hetero molecules

B: Putative aldehyde dehydrogenase family protein

hetero molecules

defined by author&software
114 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Putative aldehyde dehydrogenase family protein

hetero molecules

C: Putative aldehyde dehydrogenase family protein

hetero molecules

defined by author&software
114 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.670, 124.980, 246.200
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-934- HOH
2	1	A-1067- HOH
3	1	A-1125- HOH
4	1	A-1181- HOH
5	1	B-1028- HOH
6	1	C-936- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 2 through 78 or resid 80...
2	1	(chain B and (resid 2 through 78 or resid 80...
3	1	(chain C and (resid 2 through 78 or resid 80...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain A and (resid 2 through 78 or resid 80...	A	2 - 78
1	2	1	(chain A and (resid 2 through 78 or resid 80...	A	80 - 85
1	3	1	(chain A and (resid 2 through 78 or resid 80...	A	0 - 503
1	4	1	(chain A and (resid 2 through 78 or resid 80...	A	0 - 503
1	5	1	(chain A and (resid 2 through 78 or resid 80...	A	0 - 503
1	6	1	(chain A and (resid 2 through 78 or resid 80...	A	0 - 503
1	7	1	(chain A and (resid 2 through 78 or resid 80...	A	0 - 503
1	8	1	(chain A and (resid 2 through 78 or resid 80...	A	0 - 503
2	1	1	(chain B and (resid 2 through 78 or resid 80...	B	2 - 78
2	2	1	(chain B and (resid 2 through 78 or resid 80...	B	80 - 85
2	3	1	(chain B and (resid 2 through 78 or resid 80...	B	1 - 503
2	4	1	(chain B and (resid 2 through 78 or resid 80...	B	1 - 503
2	5	1	(chain B and (resid 2 through 78 or resid 80...	B	1 - 503
2	6	1	(chain B and (resid 2 through 78 or resid 80...	B	1 - 503
2	7	1	(chain B and (resid 2 through 78 or resid 80...	B	1 - 503
2	8	1	(chain B and (resid 2 through 78 or resid 80...	B	1 - 503
3	1	1	(chain C and (resid 2 through 78 or resid 80...	C	2 - 78
3	2	1	(chain C and (resid 2 through 78 or resid 80...	C	80 - 93
3	3	1	(chain C and (resid 2 through 78 or resid 80...	C	95 - 195
3	4	1	(chain C and (resid 2 through 78 or resid 80...	C	196
3	5	1	(chain C and (resid 2 through 78 or resid 80...	C	2 - 600
3	6	1	(chain C and (resid 2 through 78 or resid 80...	C	2 - 600
3	7	1	(chain C and (resid 2 through 78 or resid 80...	C	2 - 600
3	8	1	(chain C and (resid 2 through 78 or resid 80...	C	2 - 600

#1: Protein	Putative aldehyde dehydrogenase family protein Mass: 55031.781 Da / Num. of mol.: 3 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: BCAM2468 / Plasmid: BuceA.00020.r.B1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: B4EIN4
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-NAX / BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE Mass: 683.456 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₃₁N₇O₁₅P₂
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1188 / 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: 2.73 Å³/Da / Density % sol: 52.4 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Molecular Dimensions Morpheus screen, H2: 10% PEG 8000, 20% EG: 20mM of each amino acid: sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MES / Imidazole pH 6.5: ...Details: Molecular Dimensions Morpheus screen, H2: 10% PEG 8000, 20% EG: 20mM of each amino acid: sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MES / Imidazole pH 6.5: BuceA.00020.r.B1.PW37259 at 20mg/ml + 2.5mM NAD: cryo: direct: tray 299802h2: puck bit3-4

Crystal

Density Matthews: 2.73 Å³/Da / Density % sol: 52.4 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular Dimensions Morpheus screen, H2: 10% PEG 8000, 20% EG: 20mM of each amino acid: sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MES / Imidazole pH 6.5: ...

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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: RAYONIX MX-300 / Detector: CCD / Date: Apr 5, 2018

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: 2.1→45.813 Å / Num. obs: 99329 / % possible obs: 99.8 % / Redundancy: 4.898 % / B_iso Wilson estimate: 29.36 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.082 / R_rim(I) all: 0.092 / Χ²: 1.023 / Net I/σ(I): 12.78

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.1-2.15	5.062	0.507	3.08	7309	0.863	0.566	100
2.15-2.21	5.058	0.427	3.65	7077	0.908	0.476	100
2.21-2.28	5.07	0.363	4.35	6893	0.925	0.406	100
2.28-2.35	5.056	0.296	5.27	6745	0.949	0.331	100
2.35-2.42	5.052	0.243	6.45	6503	0.961	0.272	100
2.42-2.51	5.055	0.211	7.37	6325	0.971	0.236	100
2.51-2.6	5.044	0.175	8.75	6089	0.979	0.195	100
2.6-2.71	5.007	0.154	9.78	5849	0.983	0.172	99.9
2.71-2.83	4.988	0.122	12.06	5627	0.988	0.136	99.9
2.83-2.97	4.941	0.1	14.16	5399	0.991	0.112	99.9
2.97-3.13	4.887	0.084	16.45	5115	0.993	0.095	99.8
3.13-3.32	4.806	0.07	18.75	4856	0.995	0.079	99.9
3.32-3.55	4.704	0.06	21.21	4589	0.996	0.068	99.9
3.55-3.83	4.646	0.055	23.3	4239	0.996	0.062	99.6
3.83-4.2	4.612	0.049	25.16	3934	0.997	0.055	99.7
4.2-4.7	4.507	0.045	26.62	3576	0.997	0.051	99.8
4.7-5.42	4.555	0.044	26.65	3173	0.997	0.05	99.7
5.42-6.64	4.578	0.045	25.55	2699	0.997	0.051	99.6
6.64-9.39	4.404	0.037	27.69	2125	0.998	0.041	99.5
9.39-45.813	4.17	0.031	28.4	1207	0.998	0.036	97.3

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	(dev_3092)	refinement
PDB_EXTRACT	3.24	data extraction
SIMBAD		phasing
MoRDa		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Model identified with SIMBAD, MR done with 4pxnA as per MoRDa

Resolution: 2.1→45.813 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.14

	R_factor	Num. reflection	% reflection
R_free	0.1893	2040	2.05 %
R_work	0.1471	-	-
obs	0.1479	99314	99.84 %

Solvent computation

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

Displacement parameters

B_iso max: 98.5 Å² / B_iso mean: 34.8319 Å² / B_iso min: 13.83 Å²

Refinement step

Cycle: final / Resolution: 2.1→45.813 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11238	0	360	1198	12796
B_iso mean	-	-	42.13	40.58	-
Num. residues	-	-	-	-	1509

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	6687	X-RAY DIFFRACTION	6.819	TORSIONAL
1	2	B	6687	X-RAY DIFFRACTION	6.819	TORSIONAL
1	3	C	6687	X-RAY DIFFRACTION	6.819	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.1489	0.2514	145	0.1849	6391	6536	100
2.1489-2.2026	0.267	120	0.1792	6457	6577	100
2.2026-2.2622	0.2322	131	0.1708	6425	6556	100
2.2622-2.3287	0.2109	155	0.1598	6438	6593	100
2.3287-2.4039	0.2011	131	0.1518	6456	6587	100
2.4039-2.4898	0.2054	127	0.1527	6441	6568	100
2.4898-2.5895	0.2177	140	0.152	6426	6566	100
2.5895-2.7073	0.2236	122	0.1551	6499	6621	100
2.7073-2.85	0.2038	138	0.153	6441	6579	100
2.85-3.0285	0.2284	132	0.1573	6489	6621	100
3.0285-3.2623	0.2231	131	0.1588	6469	6600	100
3.2623-3.5905	0.1903	135	0.1496	6498	6633	100
3.5905-4.1098	0.1584	141	0.1337	6525	6666	100
4.1098-5.1767	0.1403	144	0.1172	6564	6708	100
5.1767-45.8235	0.1626	148	0.1452	6755	6903	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	1.6839	-0.0783	0.5398	0.9759	-0.5851	4.0187	-0.0574	-0.2313	-0.161	0.0984	-0.1571	-0.2506	-0.0312	0.7795	0.0633	0.2442	-0.0025	0.0356	0.4513	0.0888	0.3844	37.7735	3.261	97.559
2	0.6333	0.3156	-0.314	0.9233	-0.299	1.7795	0.0642	-0.031	-0.02	0.0871	-0.0994	-0.0868	-0.0579	0.2439	0.0486	0.1759	0.0315	-0.0117	0.2196	0.0314	0.2192	24.8368	0.5137	106.3537
3	1.0837	0.268	-0.4909	0.2597	-0.2391	0.8201	0.0011	-0.0243	-0.0556	-0.0034	-0.0674	-0.0704	0.0723	0.1475	0.059	0.2452	0.0307	-0.0037	0.1924	0.012	0.2397	16.4694	-5.0837	106.5775
4	0.4233	0.1013	-0.2243	0.3726	0.0921	0.4623	0.009	0.0432	0.062	-0.0554	0.0084	-0.0021	-0.1585	0.0939	-0.0009	0.2716	0.0084	-0.0075	0.2034	0.029	0.2364	10.0205	13.6877	101.9735
5	1.3094	0.0276	-0.5289	0.3344	0.0528	0.9203	0.0648	0.0747	0.1538	-0.0014	-0.0229	0.0267	-0.2335	0.0013	-0.0489	0.3114	-0.01	0.0068	0.1446	0.0405	0.2294	11.1652	27.3559	101.6888
6	1.5101	0.4008	0.3587	0.483	-0.004	1.2038	0.1023	-0.1346	-0.148	0.0446	-0.0846	0.0703	0.1752	-0.1368	-0.0147	0.3061	0.0178	0.0174	0.1693	-0.012	0.2468	-5.9848	-16.1135	114.3974
7	0.7726	-0.185	-0.5574	0.7533	0.5069	2.2957	0.0005	0.1074	-0.0987	0.022	-0.0423	0.1763	0.1192	-0.3396	0.0549	0.2063	-0.0275	0.0019	0.2453	-0.0331	0.3099	-26.6331	-10.9482	64.7188
8	1.4792	-0.3079	-0.6454	0.3244	0.2925	1.1179	0.017	0.1655	0.069	-0.0346	-0.0241	0.0234	-0.0097	-0.1338	-0.006	0.2189	0.0309	-0.0098	0.2073	-0.0082	0.2252	-10.3534	-5.1724	53.482
9	1.915	-0.1812	-0.2251	0.7925	-0.0467	1.1685	-0.0885	-0.0473	-0.064	0.062	0.0034	0.0959	0.0571	-0.0827	0.0866	0.1998	0.0303	0.0125	0.1812	-0.0039	0.2393	-15.9633	-9.2788	66.1207
10	1.0161	0.1534	-0.5323	0.652	-0.3113	1.1225	0.0436	0.0889	0.2141	0.0893	0.0279	0.1244	-0.2106	-0.1514	-0.0675	0.2528	0.0919	-0.0037	0.2092	0.0189	0.2903	-20.0252	21.4755	64.3381
11	1.782	0.0329	0.5188	0.5737	-0.2416	1.3889	-0.0033	0.3272	-0.3366	-0.0388	-0.0663	-0.0632	0.1861	0.1899	0.0693	0.2046	0.034	0.0228	0.1853	-0.0128	0.2427	10.8661	-12.7905	52.4574
12	0.6908	-0.1379	-0.0688	0.9693	0.3315	0.8602	0.0297	-0.4556	0.0834	0.1669	-0.038	0.1885	-0.0656	-0.2257	0.008	0.2594	-0.0699	0.0566	0.5579	-0.0493	0.2894	34.7649	-55.8804	95.7291
13	2.0572	-0.1521	-0.1703	2.7356	0.5462	1.4901	0.0557	-0.5214	0.14	0.2999	-0.055	0.2041	0.0834	-0.3325	0.0059	0.265	-0.0887	0.0666	0.585	-0.032	0.2948	32.1796	-58.0224	99.1469
14	0.7058	0.2165	-0.0433	0.7898	-0.0587	0.2959	0.0895	-0.4219	0.1884	0.2345	-0.1077	0.1068	-0.0732	-0.0415	0.0234	0.3157	-0.0833	0.015	0.5002	-0.1205	0.2871	53.8662	-42.4705	98.6138

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 0 through 24 )	A	0 - 24
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 118 )	A	25 - 118
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 225 )	A	119 - 225
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 226 through 294 )	A	226 - 294
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 295 through 465 )	A	295 - 465
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 466 through 503 )	A	466 - 503
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 92 )	B	1 - 92
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 93 through 154 )	B	93 - 154
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 155 through 258 )	B	155 - 258
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 259 through 465 )	B	259 - 465
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 466 through 503 )	B	466 - 503
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 154 )	C	2 - 154
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 155 through 225 )	C	155 - 225
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 226 through 503 )	C	226 - 503

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

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This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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

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Yorodumi