PDB-5kf0: Crystal structure of an Aldedhyde dehydrogenase from Burkholderia...

ID or keywords:

Entry

Database: PDB / ID: 5kf0

Title

Crystal structure of an Aldedhyde dehydrogenase from Burkholderia vietnamiensis

Components

Aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / Aldehyde dehydrogenase / Burkholderia thailandensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

lactaldehyde dehydrogenase (NAD+) activity / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Burkholderia vietnamiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of an Aldedhyde dehydrogenase from Burkholderia vietnamiensis
Authors: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Jun 10, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kf0.cif.gz	787.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5kf0.ent.gz	647 KB	Display	PDB format
PDBx/mmJSON format	5kf0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kf0_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5kf0_full_validation.pdf.gz	1.7 MB	Display
Data in XML	5kf0_validation.xml.gz	86.5 KB	Display
Data in CIF	5kf0_validation.cif.gz	132.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kf/5kf0 ftp://data.pdbj.org/pub/pdb/validation_reports/kf/5kf0	HTTPS FTP

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Related structure data

Related structure data	3qqaS S: Starting model for refinement
Similar structure data	6b5h-d 5jry-1 3jz4-d 3k2w-2 5j6b-d 5fhz-1 2w8p-2 5n5s-1 5mz5-d 4qyj-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.00020.o

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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) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Aldehyde dehydrogenase

B: Aldehyde dehydrogenase

C: Aldehyde dehydrogenase

D: Aldehyde dehydrogenase

hetero molecules

218 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)	83.640, 145.080, 170.030
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Aldehyde dehydrogenase / BuviA.00020.0 Mass: 53027.219 Da / Num. of mol.: 4 / Fragment: BuviA.00020.0.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria) Strain: G4 / LMG 22486 / Gene: Bcep1808_4170 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JLJ7

#1: Protein

Aldehyde dehydrogenase / BuviA.00020.0

Mass: 53027.219 Da / Num. of mol.: 4 / Fragment: BuviA.00020.0.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_4170 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JLJ7

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Non-polymers , 6 types, 2075 molecules

#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2045 / 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: 2.43 Å³/Da / Density % sol: 49 % / Mosaicity: 0.15 °
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: RigakuReagents JCSG+ screen, H5: 45% MPD, 200mM Ammonium acetate, 100mM BisTris/HCl pH 5.5; BuviA.00020.o.B1.PS37818 at 18.55mg/ml + 2mM NADP; cryo: direct; tray 269827h5, puck ehj6-1

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 31, 2016

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 226739 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / B_iso Wilson estimate: 15.96 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.069 / Net I/σ(I): 20.3

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.7-1.74	0.467	4.26	1	100
1.74-1.79	0.393	5.06	1	100
1.79-1.84	0.325	6.17	1	100
1.84-1.9	0.254	7.92	1	100
1.9-1.96	0.201	9.95	1	100
1.96-2.03	0.164	12.12	1	100
2.03-2.11	0.135	14.51	1	100
2.11-2.19	0.111	17.37	1	100
2.19-2.29	0.096	19.88	1	100
2.29-2.4	0.084	22.22	1	100
2.4-2.53	0.076	24.52	1	100
2.53-2.69	0.065	28.03	1	100
2.69-2.87	0.057	31.04	1	100
2.87-3.1	0.05	35.06	1	100
3.1-3.4	0.044	39.25	1	100
3.4-3.8	0.04	43.75	1	100
3.8-4.39	0.037	46.3	1	100
4.39-5.38	0.035	47.33	1	100
5.38-7.6	0.035	45.86	1	100
7.6-50	0.034	45.45	1	99.1

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	dev_2429	refinement
PDB_EXTRACT		data extraction
XDS		data reduction
MOLREP		phasing
ARP		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3qqa

3qqa

Resolution: 1.7→50 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.96

	R_factor	Num. reflection	% reflection
R_free	0.157	2084	9.2 %
R_work	0.1342	-	-
obs	0.1344	226662	99.96 %

Solvent computation

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

Displacement parameters

B_iso max: 71.87 Å² / B_iso mean: 19.5822 Å² / B_iso min: 7.14 Å²

Refinement step

Cycle: final / Resolution: 1.7→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14565	0	365	2083	17013
B_iso mean	-	-	25.61	31.26	-
Num. residues	-	-	-	-	1908

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	15800
X-RAY DIFFRACTION	f_angle_d	0.892	21587
X-RAY DIFFRACTION	f_chiral_restr	0.056	2417
X-RAY DIFFRACTION	f_plane_restr	0.006	2911
X-RAY DIFFRACTION	f_dihedral_angle_d	13.49	9742

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 (%)
1.7-1.7395	0.191	136	0.1574	14823	X-RAY DIFFRACTION	100
1.7395-1.7831	0.1711	125	0.154	14865	X-RAY DIFFRACTION	100
1.7831-1.8313	0.1799	133	0.1574	14845	X-RAY DIFFRACTION	100
1.8313-1.8851	0.177	144	0.1501	14830	X-RAY DIFFRACTION	100
1.8851-1.946	0.1658	145	0.1401	14899	X-RAY DIFFRACTION	100
1.946-2.0155	0.1593	128	0.1383	14869	X-RAY DIFFRACTION	100
2.0155-2.0962	0.1773	147	0.137	14896	X-RAY DIFFRACTION	100
2.0962-2.1916	0.1467	135	0.1331	14884	X-RAY DIFFRACTION	100
2.1916-2.3072	0.1499	127	0.1313	14951	X-RAY DIFFRACTION	100
2.3072-2.4517	0.1602	148	0.1361	14920	X-RAY DIFFRACTION	100
2.4517-2.641	0.1693	137	0.1355	14976	X-RAY DIFFRACTION	100
2.641-2.9067	0.1661	148	0.1368	15025	X-RAY DIFFRACTION	100
2.9067-3.3272	0.1541	136	0.1319	15095	X-RAY DIFFRACTION	100
3.3272-4.1913	0.1317	138	0.1176	15174	X-RAY DIFFRACTION	100
4.1913-41	0.1517	157	0.1325	15526	X-RAY DIFFRACTION	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	0.6561	0.2557	-0.5565	0.6686	-0.3101	2.6332	-0.0112	0.0077	0.1197	0.0769	0.0112	-0.102	-0.2468	-0.0046	-0.0101	0.1297	-0.0186	-0.0325	0.087	-0.0088	0.1808	45.9592	34.8954	-29.7907
2	0.5295	0.3053	-0.3052	0.9593	-0.579	0.7007	0.0017	0.0345	0.0751	0.0229	0.0156	0.0042	-0.0598	-0.0329	-0.0511	0.1108	0.0013	-0.0035	0.0989	-0.0106	0.1058	29.0644	22.1945	-26.7273
3	0.3109	0.0904	0.0871	0.5382	0.0729	0.4486	-0.0267	0.0441	0.0616	-0.0631	-0.0001	-0.0292	-0.0424	0.0085	0.0212	0.1028	-0.0122	0.0087	0.0879	0.0069	0.0988	38.2981	20.5216	-42.5729
4	0.3157	-0.0223	-0.0402	0.4025	-0.2681	0.8086	-0.0192	0.073	-0.0074	-0.1007	-0.0017	-0.0482	0.0001	0.056	0.0206	0.1248	-0.0083	0.0177	0.1026	-0.01	0.1108	36.0813	9.8217	-47.8527
5	1.3653	-0.424	0.1612	0.6119	0.097	0.8304	0.0083	-0.0683	-0.1911	0.0061	0.004	-0.038	0.122	0.0214	-0.0259	0.1205	-0.0036	0.0145	0.0629	0.012	0.1427	42.3198	-20.0809	-22.5643
6	0.8125	-0.4729	0.1388	0.6838	-0.3354	0.2653	-0.01	0.0047	-0.0089	-0.0514	-0.0178	-0.0518	-0.0057	0.0316	0.0239	0.1117	0.006	0.0048	0.1024	-0.0136	0.1015	40.1048	-7.3928	-28.6827
7	0.4697	-0.1306	-0.1491	0.5131	-0.1321	1.0843	-0.0609	-0.1882	-0.0526	0.1506	0.0596	-0.0531	0.0659	0.0589	0.0016	0.1217	0.0254	-0.0231	0.1618	0.0085	0.1122	46.2034	-3.9129	-0.1877
8	0.4596	-0.125	0.134	0.3801	-0.1981	0.7671	-0.0397	-0.108	0.0184	0.0894	0.021	-0.0817	-0.0351	0.1352	0.021	0.0962	0.0125	-0.0139	0.1208	-0.0122	0.1042	45.5686	2.5119	-6.3117
9	0.9663	-0.1741	-0.066	0.5582	0.1259	0.9375	0.0129	0.0136	0.1974	-0.0329	0.0113	0.1488	-0.1848	-0.0766	-0.0205	0.1445	0.0274	0	0.0924	0.0112	0.1956	-2.7206	31.4283	-23.7033
10	0.6903	-0.2426	-0.2206	0.9506	0.248	0.2961	0.0147	-0.0356	0.1124	0.0123	-0.0011	0.0311	-0.0559	-0.0123	-0.023	0.1028	0.0186	-0.008	0.1064	-0.0077	0.1015	6.4888	18.2536	-23.3038
11	0.4242	0.0727	0.4028	0.4364	0.0008	0.8816	-0.0258	-0.0289	0.0894	0.0983	-0.0075	0.0942	-0.1087	-0.0382	0.0511	0.1324	0.0316	0.0375	0.1152	-0.0209	0.129	2.417	21.7911	-3.2475
12	0.2465	0.0751	0.0631	0.5556	0.2088	0.7125	-0.0041	-0.0756	0.0276	0.1551	-0.0265	0.1067	-0.0353	-0.1119	0.0299	0.1227	0.0247	0.0365	0.1116	-0.0107	0.1104	5.2824	14.1653	0.0789
13	1.2136	0.4146	0.3458	0.4612	0.011	1.2093	0.0613	-0.0899	-0.2986	0.0545	0.0289	0.0224	0.178	-0.0995	-0.0932	0.1374	0.0015	0.002	0.0958	0.0313	0.2004	2.1235	-22.9438	-13.167
14	0.8849	0.3947	0.1162	0.8613	0.1171	0.2712	0.0144	-0.0039	-0.1297	0.0341	0.0057	0.0179	0.0172	-0.051	-0.0304	0.0933	0.0076	0.0141	0.1091	0.0081	0.0883	5.7197	-10.05	-15.4447
15	0.5695	0.1235	-0.179	0.5041	0.0493	1.0543	-0.0457	0.1041	-0.1062	-0.0871	0.0612	0.0218	0.1328	-0.0508	-0.0023	0.1086	-0.0165	-0.0071	0.1532	-0.016	0.1402	-1.5854	-13.6194	-41.6858
16	0.444	0.1666	0.1633	0.3962	0.1731	0.6136	-0.0234	0.0636	-0.0304	-0.053	0.0218	0.0744	0.018	-0.1467	0.0067	0.0908	-0.0024	-0.0004	0.1409	0.0021	0.1156	-1.7318	-5.5096	-37.5847

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 -2 through 61 )	A	-2 - 61
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 62 through 143 )	A	62 - 143
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 144 through 329 )	A	144 - 329
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 330 through 477 )	A	330 - 477
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 117 )	B	2 - 117
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 118 through 230 )	B	118 - 230
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 231 through 329 )	B	231 - 329
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 330 through 477 )	B	330 - 477
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 94 )	C	2 - 94
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 95 through 195 )	C	95 - 195
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 196 through 329 )	C	196 - 329
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 330 through 477 )	C	330 - 477
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 2 through 94 )	D	2 - 94
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 95 through 230 )	D	95 - 230
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 231 through 329 )	D	231 - 329
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 330 through 477 )	D	330 - 477

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