PDB-4o6r: Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkh...

ID or keywords:

Entry

Database: PDB / ID: 4o6r

Title

Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia

Components

Aldehyde Dehydrogenase

Keywords

OXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

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

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia
Authors: Dranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.

History

Deposition	Dec 23, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 20, 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 / 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 / _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	4o6r.cif.gz	764 KB	Display	PDBx/mmCIF format
PDB format	pdb4o6r.ent.gz	629.5 KB	Display	PDB format
PDBx/mmJSON format	4o6r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4o6r_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	4o6r_full_validation.pdf.gz	1.9 MB	Display
Data in XML	4o6r_validation.xml.gz	89.1 KB	Display
Data in CIF	4o6r_validation.cif.gz	137.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o6/4o6r ftp://data.pdbj.org/pub/pdb/validation_reports/o6/4o6r	HTTPS FTP

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Related structure data

Related structure data	4yweC 4go4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ekc-2 4h73-5 5ek6-1 5exf-1 4i26-d 3rhj-d 4dal-1 5eeb-1 1bpw-d 2o2r-d 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.y

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Aldehyde Dehydrogenase

B: Aldehyde Dehydrogenase

C: Aldehyde Dehydrogenase

D: Aldehyde Dehydrogenase

hetero molecules

216 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)	112.130, 125.610, 150.850
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Aldehyde Dehydrogenase Mass: 53299.270 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610 Gene: BCAM0469 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EJX1

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Non-polymers , 5 types, 2186 molecules

#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2161 / 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: 2.49 Å³/Da / Density % sol: 50.63 %
Crystal grow	Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus(c3): glycerol, peg4000, sodium nitrate, sodium phosphate, ammonium sulfate, imidazole, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97857 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2013 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. all: 167640 / Num. obs: 167523 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / R_merge(I) obs: 0.107 / Net I/σ(I): 15.56

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.9-1.95		0.48	4.39	1	99.8
1.95-2		0.4	5.21	1	99.9
2-2.06		0.339	6.17	1	100
2.06-2.12		0.283	7.26	1	99.9
2.12-2.19		0.239	8.45	1	100
2.19-2.27		0.204	9.8	1	99.9
2.27-2.36		0.179	10.95	1	100
2.36-2.45		0.164	11.82	1	100
2.45-2.56		0.141	13.51	1	100
2.56-2.69		0.125	15.03	1	100
2.69-2.83		0.105	17.32	1	100
2.83-3		0.088	19.62	1	100
3-3.21		0.073	22.8	1	99.9
3.21-3.47		0.06	26.53	1	100
3.47-3.8		0.049	31.01	1	100
3.8-4.25		0.043	33.98	1	99.9
4.25-4.91		0.035	36.92	1	99.9
4.91-6.01		0.038	33.23	1	100
6.01-8.5		0.034	34.6	1	100
	8.5	0.024	39.77	1	98.6

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	48.48 Å
Translation	2.5 Å	48.48 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.2	phasing
REFMAC	5.8.0049	refinement
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4GO4

4go4

Resolution: 1.9→19.86 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.961 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.081 / SU ML: 0.079 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18209	8408	5 %	RANDOM
R_work	0.15061	-	-	-
obs	0.15218	158858	99.83 %	-
all	-	175674	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 14.272 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.05 Å²	-0 Å²	0 Å²
2-	-	-0.1 Å²	0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14700	0	184	2161	17045

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	15683
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	14868
X-RAY DIFFRACTION	r_angle_refined_deg	1.441	1.96	21411
X-RAY DIFFRACTION	r_angle_other_deg	0.802	3	34080
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.906	5	2076
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.596	23.304	693
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.389	15	2387
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.144	15	134
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2379
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	18358
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3700
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.484	0.687	8042
X-RAY DIFFRACTION	r_mcbond_other	0.484	0.687	8041
X-RAY DIFFRACTION	r_mcangle_it	0.837	1.028	10106
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.916	0.861	7641
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.239	609	-
R_work	0.199	11491	-
obs	-	-	99.79 %

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	0.6197	0.2118	0.0495	1.0368	0.3548	0.5544	-0.0605	0.1442	-0.0143	-0.1605	0.0603	-0.0564	-0.0022	0.0673	0.0002	0.076	-0.0165	0.0239	0.0791	-0.0078	0.0081	96.5275	93.9015	9.6982
2	0.2557	0.1099	0.0289	0.2538	0.0363	0.2079	-0.0268	0.0619	-0.0382	-0.0632	0.0226	-0.0281	0.0319	0.0245	0.0043	0.0452	-0.0027	0.0119	0.0525	-0.0043	0.0251	98.2078	96.6073	23.3488
3	0.51	-0.0002	-0.1885	0.7057	0.0775	0.5756	-0.0417	0.026	-0.1078	-0.0332	-0.0021	0.0344	0.0514	0.0137	0.0439	0.0279	-0.0089	0.0009	0.0216	-0.0117	0.0651	76.7274	73.9368	24.4252
4	0.505	0.2412	0.2366	0.5005	0.2	0.2675	0.0144	-0.0087	-0.008	0.0164	-0.0087	-0.0015	0.031	-0.0112	-0.0057	0.0237	0.0064	0.0094	0.0383	0.0047	0.0175	91.2684	101.4077	36.6893
5	1.4941	1.1228	0.0599	1.7529	-0.642	0.6632	-0.037	0.1362	0.0092	-0.0791	0.111	0.0245	0.0186	-0.0835	-0.074	0.0692	-0.0016	-0.0114	0.1056	0.0275	0.034	64.8514	133.1198	5.4902
6	0.1874	-0.0064	-0.0147	0.2428	-0.1213	0.3142	-0.0101	0.0467	0.015	-0.0433	0.0248	0.0196	-0.0033	-0.0232	-0.0147	0.0429	-0.0105	-0.0097	0.0469	0.0103	0.0237	71.4333	123.6173	19.1924
7	0.7791	0.0548	0.2715	0.5573	-0.0706	0.6461	-0.0459	0.021	0.1338	-0.0025	0.0028	-0.0142	-0.0499	-0.0102	0.0431	0.016	-0.0039	-0.0091	0.0203	0.0037	0.0546	91.2286	146.1294	24.8513
8	0.5071	0.1749	-0.1757	0.3759	-0.1049	0.1443	0.0143	-0.014	0.013	0.0371	-0.0016	0.0257	-0.026	0.0337	-0.0127	0.0305	0.0037	-0.006	0.043	0.0004	0.022	76.9326	118.6726	36.7996
9	0.4165	-0.0128	0.2256	0.2106	-0.0083	0.4103	0.0039	-0.0691	-0.0363	0.0289	0.0011	-0.0052	0.0483	0.005	-0.005	0.0395	0.0017	0.0066	0.0551	0.0139	0.0178	96.3725	95.7189	57.599
10	4.3694	4.3601	-0.7875	5.401	-1.11	0.243	0.1374	-0.0654	-0.1596	0.0633	-0.2143	-0.3065	0.0058	0.0573	0.0769	0.0786	0.0066	-0.0003	0.0579	0.0091	0.0628	105.2135	90.1635	41.9082
11	0.5581	-0.0167	0.1088	0.6554	-0.3236	0.9136	-0.0169	-0.0079	0.0455	0.0473	-0.0555	-0.1367	-0.0065	0.0905	0.0724	0.0088	-0.0038	-0.0237	0.0508	0.0095	0.0792	122.5696	112.6149	51.8921
12	0.6002	0.2602	0.1547	0.4458	0.0856	0.0652	-0.013	0.0231	0.0062	-0.0075	0.0006	-0.0295	-0.0009	0.0192	0.0124	0.0366	0.0098	0.0021	0.0433	0.0049	0.0297	98.5002	106.8986	36.4833
13	1.916	0.2526	-0.0176	1.2505	0.6118	0.4269	0.1086	-0.3502	0.2971	0.204	-0.0518	0.0438	-0.0371	0.0347	-0.0568	0.2173	-0.0221	0.0531	0.1586	-0.0737	0.0867	69.2899	134.5638	68.1122
14	0.4495	-0.0031	-0.1064	0.1754	0.0109	0.1595	-0.0186	-0.1027	0.0271	0.0395	0.0129	0.0227	-0.0139	-0.0027	0.0057	0.0341	0.0099	0.0031	0.0523	-0.0063	0.0206	65.498	118.5325	54.6715
15	1.0606	0.0768	1.1976	1.0305	0.9163	3.2975	-0.0562	-0.1536	0.0207	0.0951	-0.0663	0.2201	-0.0029	-0.2693	0.1226	0.0238	0.0031	0.0455	0.0785	-0.014	0.1058	39.6154	114.1784	56.8606
16	0.647	0.1952	-0.1283	0.2905	-0.0481	0.1023	-0.0097	0.0013	-0.0055	0.0025	-0.0008	0.0474	0.0043	-0.0311	0.0105	0.0284	0.0086	-0.0027	0.0356	-0.0061	0.0319	63.2094	112.1929	37.9438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 114
2	X-RAY DIFFRACTION	2	A	115 - 256
3	X-RAY DIFFRACTION	3	A	257 - 435
4	X-RAY DIFFRACTION	4	A	436 - 488
5	X-RAY DIFFRACTION	5	B	8 - 36
6	X-RAY DIFFRACTION	6	B	37 - 255
7	X-RAY DIFFRACTION	7	B	256 - 435
8	X-RAY DIFFRACTION	8	B	436 - 488
9	X-RAY DIFFRACTION	9	C	8 - 232
10	X-RAY DIFFRACTION	10	C	233 - 257
11	X-RAY DIFFRACTION	11	C	258 - 404
12	X-RAY DIFFRACTION	12	C	405 - 488
13	X-RAY DIFFRACTION	13	D	8 - 25
14	X-RAY DIFFRACTION	14	D	26 - 335
15	X-RAY DIFFRACTION	15	D	336 - 375
16	X-RAY DIFFRACTION	16	D	376 - 488

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