PDB-4h7n: The Structure of Putative Aldehyde Dehydrogenase PutA from Anabae...

ID or keywords:

Entry

Database: PDB / ID: 4h7n

Title

The Structure of Putative Aldehyde Dehydrogenase PutA from Anabaena variabilis.

Components

Aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ALDH_DDALDH / COG1012 / Glyco_hydro_97 /

human microbiome

Function / homology

Function and homology information

glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity /

aldehyde dehydrogenase (NAD+) /

aldehyde dehydrogenase (NAD+) activity
Similarity search - Function

Biological species

Anabaena variabilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2 Å

Authors

Cuff, M.E. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The Structure of Putative Aldehyde Dehydrogenase PutA from Anabaena variabilis.
Authors: Cuff, M.E. / Chhor, G. / Clancy, S. / Joachimiak, A.

History

Deposition	Sep 20, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 10, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2012	Group: Database references / Structure summary
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4h7n.cif.gz	734.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4h7n.ent.gz	633.3 KB	Display	PDB format
PDBx/mmJSON format	4h7n.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/h7/4h7n ftp://data.pdbj.org/pub/pdb/validation_reports/h7/4h7n	HTTPS FTP

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Related structure data

Similar structure data	4nea-2 4nmk-2 4nmj-3 2vro-d 4nmk-3 4nmj-2 4h73-3 5u0m-d 4nmj-1 6wsb-d 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: MCSG-apc100005

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (6) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (6)

Deposited unit

A: Aldehyde dehydrogenase

B: Aldehyde dehydrogenase

C: Aldehyde dehydrogenase

D: Aldehyde dehydrogenase

hetero molecules

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

1

A: Aldehyde dehydrogenase

D: Aldehyde dehydrogenase

hetero molecules

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

2

B: Aldehyde dehydrogenase

C: Aldehyde dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.841, 88.513, 123.001
Angle α, β, γ (deg.)	90.000, 109.970, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

Very likely the dimers observed in the asymmetric unit: B & C, A & D

#1: Protein	Aldehyde dehydrogenase / Mass: 52182.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / Gene: Ava_2258 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q3MAW0, aldehyde dehydrogenase (NAD+)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1201 / 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: 2.59 Å³/Da / Density % sol: 52.59 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 24% PEG 1500, 20% Glycerol, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97931, 0.97948

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2011

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97931	1
2	0.97948	1

Reflection

Redundancy: 7.5 % / Av σ(I) over netI: 26.98 / Number: 1075146 / R_merge(I) obs: 0.102 / Χ²: 1.44 / D res high: 2 Å / D res low: 50 Å / Num. obs: 143525 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.43	50	97.9	1	0.075	5.239	7.1
4.31	5.43	99.9	1	0.064	3.385	7.3
3.76	4.31	100	1	0.069	2.92	7.3
3.42	3.76	100	1	0.081	2.725	7.3
3.17	3.42	100	1	0.091	2.159	7.4
2.99	3.17	100	1	0.1	1.66	7.5
2.84	2.99	100	1	0.111	1.388	7.5
2.71	2.84	100	1	0.121	1.121	7.6
2.61	2.71	100	1	0.136	0.956	7.6
2.52	2.61	100	1	0.154	0.901	7.6
2.44	2.52	100	1	0.178	0.811	7.6
2.37	2.44	100	1	0.203	0.761	7.6
2.31	2.37	100	1	0.23	0.725	7.6
2.25	2.31	100	1	0.262	0.69	7.6
2.2	2.25	100	1	0.295	0.655	7.6
2.15	2.2	100	1	0.355	0.64	7.6
2.11	2.15	100	1	0.401	0.612	7.6
2.07	2.11	100	1	0.478	0.622	7.6
2.03	2.07	100	1	0.538	0.605	7.6
2	2.03	100	1	0.642	0.62	7.5

Reflection

Resolution: 2→50 Å / Num. all: 143525 / Num. obs: 143525 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / B_iso Wilson estimate: 28.1 Å² / R_merge(I) obs: 0.102 / Χ²: 1.441 / Net I/σ(I): 6.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2-2.03	7.5	0.642	7138	0.62	1	100
2.03-2.07	7.6	0.538	7155	0.605	1	100
2.07-2.11	7.6	0.478	7119	0.622	1	100
2.11-2.15	7.6	0.401	7201	0.612	1	100
2.15-2.2	7.6	0.355	7120	0.64	1	100
2.2-2.25	7.6	0.295	7140	0.655	1	100
2.25-2.31	7.6	0.262	7152	0.69	1	100
2.31-2.37	7.6	0.23	7170	0.725	1	100
2.37-2.44	7.6	0.203	7179	0.761	1	100
2.44-2.52	7.6	0.178	7176	0.811	1	100
2.52-2.61	7.6	0.154	7148	0.901	1	100
2.61-2.71	7.6	0.136	7148	0.956	1	100
2.71-2.84	7.6	0.121	7204	1.121	1	100
2.84-2.99	7.5	0.111	7170	1.388	1	100
2.99-3.17	7.5	0.1	7183	1.66	1	100
3.17-3.42	7.4	0.091	7197	2.159	1	100
3.42-3.76	7.3	0.081	7205	2.725	1	100
3.76-4.31	7.3	0.069	7225	2.92	1	100
4.31-5.43	7.3	0.064	7243	3.385	1	99.9
5.43-50	7.1	0.075	7252	5.239	1	97.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 2→41.33 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.955 / WR_factor R_free: 0.1902 / WR_factor R_work: 0.1533 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8965 / SU B: 6.721 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1473 / SU R_free: 0.1356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1957	7172	5 %	RANDOM
R_work	0.1559	-	-	-
all	0.1579	143358	-	-
obs	0.1579	143358	99.47 %	-

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 max: 93.27 Å² / B_iso mean: 36.2349 Å² / B_iso min: 17.09 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.58 Å²	0 Å²	0.28 Å²
2-	-	1.42 Å²	0 Å²
3-	-	-	-2.46 Å²

Refinement step

Cycle: LAST / Resolution: 2→41.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14395	0	90	1201	15686

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	14824
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	14423
X-RAY DIFFRACTION	r_angle_refined_deg	1.659	1.976	20164
X-RAY DIFFRACTION	r_angle_other_deg	0.831	3	33121
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.141	5	1887
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.775	24.049	615
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.88	15	2316
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.974	15	98
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	2335
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	16753
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3289

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.26	511	-
R_work	0.207	9681	-
all	-	10192	-
obs	-	-	96.41 %

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	1.4564	-1.518	-2.9921	2.2673	2.8418	6.6792	-0.1126	0.0829	-0.2898	-0.076	-0.2082	0.2802	0.2322	-0.1062	0.3208	0.1434	-0.0372	0.0099	0.0687	-0.0028	0.2567	42.9226	14.0186	71.6605
2	2.7021	0.5656	-0.3407	0.8707	-0.1179	0.5827	-0.0692	0.3732	0.2645	-0.1176	0.0707	0.0892	-0.0417	-0.1599	-0.0016	0.07	-0.0021	-0.0713	0.0764	0.035	0.0965	52.2568	36.7307	70.6216
3	2.0903	0.3109	-0.1577	0.365	-0.0405	0.568	-0.0341	0.1303	-0.0225	-0.0814	0.0146	-0.0042	-0.0361	-0.0509	0.0195	0.0575	-0.0135	-0.0472	0.0295	0.0042	0.0782	60.7314	30.5483	75.121
4	0.9919	0.1318	-0.1261	0.8576	0.4253	1.4305	-0.0423	-0.1607	-0.0951	0.1787	-0.0567	0.1641	0.1398	-0.168	0.0989	0.0554	-0.0188	0.0127	0.089	0.0355	0.1519	40.2967	25.5789	100.2058
5	2.1958	-0.336	-1.3028	0.9557	1.1101	2.1931	0.0456	-0.1655	0.0691	0.105	-0.0158	0.0232	-0.0845	0.0418	-0.0298	0.0883	-0.0066	-0.0279	0.0763	0.0158	0.109	55.6866	35.8958	101.8264
6	3.4675	0.4497	-0.9533	0.9624	0.3222	0.6121	-0.0497	-0.0052	0.3134	-0.1614	0.15	-0.1851	-0.1972	0.1371	-0.1003	0.1792	-0.0874	-0.0482	0.0549	0.0119	0.178	82.4141	45.3268	76.0826
7	11.1765	4.5484	-1.3672	2.3748	-1.2551	1.8019	0.2471	-0.6007	0.3367	0.2804	-0.3497	0.1017	-0.3732	-0.0733	0.1025	0.1172	0.0062	-0.0161	0.2146	-0.1273	0.1577	18.1616	86.088	119.7892
8	1.432	-0.2335	-0.228	0.6415	0.0141	1.178	-0.0736	-0.2679	-0.0895	0.0889	-0.0422	-0.0563	0.0378	0.0395	0.1158	0.0321	-0.0024	-0.0286	0.1268	-0.0161	0.1022	32.936	69.4159	113.1327
9	0.6436	-0.0796	-0.4255	0.4222	-0.1122	0.8985	0.0028	-0.104	-0.0231	0.0478	-0.0726	0.0512	-0.0015	-0.0935	0.0698	0.0236	-0.0143	-0.0341	0.1064	-0.0401	0.1191	27.344	71.1478	103.7472
10	0.8823	-0.3169	-0.1895	0.6118	0.2802	1.6513	-0.0198	-0.0279	0.0142	0.0655	-0.0648	0.2278	-0.0197	-0.5158	0.0847	0.0158	0.0049	0.0032	0.2938	-0.0932	0.234	-4.1887	72.7538	104.2116
11	1.5526	0.4557	0.0034	1.3069	0.0122	1.0208	0.0634	0.1355	-0.1583	-0.0114	-0.0985	0.1612	0.1123	-0.2918	0.0351	0.0226	-0.0337	-0.0218	0.181	-0.0938	0.1676	6.786	64.3875	91.0374
12	1.7163	0.0106	-0.445	0.4366	-0.2997	0.7284	0.0085	-0.1737	-0.178	-0.2076	-0.0847	-0.0516	0.1146	0.1094	0.0761	0.1129	0.0402	-0.0105	0.0338	0.0211	0.1147	45.4109	62.7175	81.6959
13	0.9454	0.2437	-0.2339	0.4935	0.1874	1.1387	-0.0904	0.1108	-0.008	-0.1417	-0.0206	0.0719	0.026	-0.201	0.111	0.08	0.0065	-0.0664	0.0804	-0.0162	0.1191	26.5037	70.65	62.8518
14	0.636	0.1029	-0.5138	0.378	0.1325	1.0504	-0.0972	0.0554	-0.0407	-0.0814	-0.0535	0.0544	0.0986	-0.2387	0.1507	0.0652	-0.0033	-0.0485	0.1156	-0.0374	0.1255	22.6486	68.5674	71.4291
15	1.0037	-0.5171	0.0039	0.5115	0.3285	2.1436	0.0188	0.0016	0.1459	-0.0767	-0.1112	0.0848	-0.1922	-0.1572	0.0924	0.0368	0.0307	-0.0434	0.0967	-0.0411	0.1619	25.6069	82.1794	78.2449
16	0.8045	0.2622	-0.0271	0.8248	-0.3688	1.3335	-0.0317	-0.0602	0.0723	-0.1364	-0.0568	-0.1499	0.0123	0.1416	0.0884	0.0595	0.0168	-0.0131	0.0423	0.0165	0.1339	56.0324	79.3286	72.1974
17	1.3316	0.0383	-0.2695	1.3136	-0.1197	1.0967	0.0047	-0.2485	-0.1192	0.015	-0.041	-0.0762	0.0973	0.1348	0.0363	0.0354	0.0222	-0.0331	0.0771	0.0317	0.1071	50.4919	68.4182	85.7656
18	1.1731	0.2761	-0.6052	0.6378	0.1264	0.9609	-0.0657	0.0254	-0.2199	0.0885	-0.0703	0.0871	0.1794	-0.2074	0.136	0.0656	-0.0322	-0.0161	0.1246	-0.0212	0.1635	18.8923	63.0823	90.7535
19	1.083	0.0816	-0.1114	0.8869	0.0774	1.1969	-0.0194	-0.1621	0.0378	-0.0188	0.0576	-0.1476	-0.0738	0.2919	-0.0381	0.0184	-0.0284	-0.0303	0.122	-0.0084	0.1375	91.4979	35.1848	99.7386
20	11.2004	-3.3716	3.9656	4.4548	0.8969	2.6803	0.2492	0.4624	0.3519	-0.196	-0.279	-0.2577	-0.0151	0.0596	0.0298	0.1596	0.0713	-0.0037	0.096	0.0642	0.2199	53.4191	49.8607	94.4337
21	0.9811	0.2782	0.1259	0.6939	0.3177	0.9398	0.0021	-0.0767	-0.0479	-0.0296	0.0229	-0.0947	0.013	0.1937	-0.025	0.0162	-0.0048	-0.0302	0.0858	0.0165	0.1027	84.7897	29.3718	95.6486
22	1.7107	0.3538	-0.4038	1.0248	-0.3947	1.551	-0.3138	0.0623	-0.0311	-0.5027	0.3139	-0.3476	0.1187	0.173	-0.0001	0.2766	-0.1791	0.146	0.1736	-0.0944	0.2285	101.2622	31.9516	69.4739
23	2.2753	0.9389	-0.7976	2.1554	-0.1098	0.7511	-0.2246	0.2657	0.19	-0.4077	0.3482	-0.0348	-0.1618	-0.0041	-0.1236	0.2068	-0.1301	-0.0287	0.1049	0.0405	0.109	84.037	40.0382	71.015
24	1.9371	0.0156	-0.2067	0.5231	0.3375	0.5115	0.041	-0.0034	0.1329	-0.0545	-0.0275	0.1942	-0.1244	-0.1082	-0.0134	0.0872	0.0211	-0.0282	0.0819	0.0353	0.1824	54.7205	42.2877	96.1285

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 21
2	X-RAY DIFFRACTION	2	A	22 - 106
3	X-RAY DIFFRACTION	3	A	107 - 230
4	X-RAY DIFFRACTION	4	A	231 - 370
5	X-RAY DIFFRACTION	5	A	371 - 441
6	X-RAY DIFFRACTION	6	A	442 - 470
7	X-RAY DIFFRACTION	7	B	2 - 23
8	X-RAY DIFFRACTION	8	B	24 - 73
9	X-RAY DIFFRACTION	9	B	74 - 230
10	X-RAY DIFFRACTION	10	B	231 - 373
11	X-RAY DIFFRACTION	11	B	374 - 446
12	X-RAY DIFFRACTION	12	B	447 - 471
13	X-RAY DIFFRACTION	13	C	2 - 106
14	X-RAY DIFFRACTION	14	C	107 - 186
15	X-RAY DIFFRACTION	15	C	187 - 230
16	X-RAY DIFFRACTION	16	C	231 - 373
17	X-RAY DIFFRACTION	17	C	374 - 428
18	X-RAY DIFFRACTION	18	C	429 - 470
19	X-RAY DIFFRACTION	19	D	3 - 105
20	X-RAY DIFFRACTION	20	D	106 - 119
21	X-RAY DIFFRACTION	21	D	120 - 230
22	X-RAY DIFFRACTION	22	D	231 - 374
23	X-RAY DIFFRACTION	23	D	375 - 446
24	X-RAY DIFFRACTION	24	D	447 - 470

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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